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dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

All alleles are reported in the Forward orientation. Click on the Variant Details tab for details on Genomic Placement, Gene, and Amino Acid changes. HGVS names are in the HGVS tab.

Reference SNP (rs) Report

This page reports data for a single dbSNP Reference SNP variation (RefSNP or rs) from the new redesigned dbSNP build.
Top of the page reports a concise summary for the rs, with more specific details included in the corresponding tabs below.
All alleles are reported in the Forward orientation. Use the Genomic View to inspect the nucleotides flanking the variant, and its neighbors.
For more information see Help documentation.

rs774465428

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr3:49902955 (GRCh38.p14) Help

The anchor position for this RefSNP. Includes all nucleotides potentially affected by this change, thus it can differ from HGVS, which is right-shifted. See here for details.

Alleles
T>C
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.000004 (1/250070, GnomAD_exome)
C=0.000008 (1/118728, ExAC)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
MST1R : Missense Variant
Publications
0 citations
Genomic View
See rs on genome
Help

Frequency tab displays a table of the reference and alternate allele frequencies reported by various studies and populations. Table lines, where Population="Global" refer to the entire study population, whereas lines, where Group="Sub", refer to a study-specific population subgroupings (i.e. AFR, CAU, etc.), if available. Frequency for the alternate allele (Alt Allele) is a ratio of samples observed-to-total, where the numerator (observed samples) is the number of chromosomes in the study with the minor allele present (found in "Sample size", where Group="Sub"), and the denominator (total samples) is the total number of all chromosomes in the study for the variant (found in "Sample size", where Group="Study-wide" and Population="Global").

Download
Study Population Group Sample Size Ref Allele Alt Allele
gnomAD - Exomes Global Study-wide 250070 T=0.999996 C=0.000004
gnomAD - Exomes European Sub 134410 T=1.000000 C=0.000000
gnomAD - Exomes Asian Sub 48890 T=0.99998 C=0.00002
gnomAD - Exomes American Sub 34538 T=1.00000 C=0.00000
gnomAD - Exomes African Sub 16082 T=1.00000 C=0.00000
gnomAD - Exomes Ashkenazi Jewish Sub 10036 T=1.00000 C=0.00000
gnomAD - Exomes Other Sub 6114 T=1.0000 C=0.0000
ExAC Global Study-wide 118728 T=0.999992 C=0.000008
ExAC Europe Sub 71410 T=1.00000 C=0.00000
ExAC Asian Sub 24930 T=0.99996 C=0.00004
ExAC American Sub 11478 T=1.00000 C=0.00000
ExAC African Sub 10032 T=1.00000 C=0.00000
ExAC Other Sub 878 T=1.000 C=0.000
Help

Variant Details tab shows known variant placements on genomic sequences: chromosomes (NC_), RefSeqGene, pseudogenes or genomic regions (NG_), and in a separate table: on transcripts (NM_) and protein sequences (NP_). The corresponding transcript and protein locations are listed in adjacent lines, along with molecular consequences from Sequence Ontology. When no protein placement is available, only the transcript is listed. Column "Codon[Amino acid]" shows the actual base change in the format of "Reference > Alternate" allele, including the nucleotide codon change in transcripts, and the amino acid change in proteins, respectively, allowing for known ribosomal slippage sites. To view nucleotides adjacent to the variant use the Genomic View at the bottom of the page - zoom into the sequence until the nucleotides around the variant become visible.

Genomic Placements
Sequence name Change
GRCh38.p14 chr 3 NC_000003.12:g.49902955T>C
GRCh37.p13 chr 3 NC_000003.11:g.49940388T>C
MST1R RefSeqGene NG_030322.1:g.5919A>G
Gene: MST1R, macrophage stimulating 1 receptor (minus strand)
Molecule type Change Amino acid[Codon] SO Term
MST1R transcript variant 1 NM_002447.4:c.655A>G R [AGG] > G [GGG] Coding Sequence Variant
macrophage-stimulating protein receptor isoform 1 preproprotein NP_002438.2:p.Arg219Gly R (Arg) > G (Gly) Missense Variant
MST1R transcript variant 2 NM_001244937.3:c.655A>G R [AGG] > G [GGG] Coding Sequence Variant
macrophage-stimulating protein receptor isoform 2 precursor NP_001231866.1:p.Arg219Gly R (Arg) > G (Gly) Missense Variant
MST1R transcript variant 3 NM_001318913.2:c.655A>G R [AGG] > G [GGG] Coding Sequence Variant
macrophage-stimulating protein receptor isoform 3 precursor NP_001305842.1:p.Arg219Gly R (Arg) > G (Gly) Missense Variant
MST1R transcript variant 4 NR_134919.2:n.919A>G N/A Non Coding Transcript Variant
MST1R transcript variant X1 XM_005265170.5:c.655A>G R [AGG] > G [GGG] Coding Sequence Variant
macrophage-stimulating protein receptor isoform X1 XP_005265227.2:p.Arg219Gly R (Arg) > G (Gly) Missense Variant
MST1R transcript variant X2 XM_011533739.3:c.655A>G R [AGG] > G [GGG] Coding Sequence Variant
macrophage-stimulating protein receptor isoform X2 XP_011532041.1:p.Arg219Gly R (Arg) > G (Gly) Missense Variant
MST1R transcript variant X3 XM_047448162.1:c.655A>G R [AGG] > G [GGG] Coding Sequence Variant
macrophage-stimulating protein receptor isoform X3 XP_047304118.1:p.Arg219Gly R (Arg) > G (Gly) Missense Variant
MST1R transcript variant X4 XM_011533740.3:c.655A>G R [AGG] > G [GGG] Coding Sequence Variant
macrophage-stimulating protein receptor isoform X4 XP_011532042.1:p.Arg219Gly R (Arg) > G (Gly) Missense Variant
MST1R transcript variant X5 XM_011533741.3:c.655A>G R [AGG] > G [GGG] Coding Sequence Variant
macrophage-stimulating protein receptor isoform X5 XP_011532043.1:p.Arg219Gly R (Arg) > G (Gly) Missense Variant
MST1R transcript variant X6 XM_047448163.1:c.655A>G R [AGG] > G [GGG] Coding Sequence Variant
macrophage-stimulating protein receptor isoform X6 XP_047304119.1:p.Arg219Gly R (Arg) > G (Gly) Missense Variant
MST1R transcript variant X8 XM_011533742.3:c.655A>G R [AGG] > G [GGG] Coding Sequence Variant
macrophage-stimulating protein receptor isoform X7 XP_011532044.1:p.Arg219Gly R (Arg) > G (Gly) Missense Variant
MST1R transcript variant X9 XM_047448164.1:c.655A>G R [AGG] > G [GGG] Coding Sequence Variant
macrophage-stimulating protein receptor isoform X8 XP_047304120.1:p.Arg219Gly R (Arg) > G (Gly) Missense Variant
MST1R transcript variant X10 XM_011533743.3:c.655A>G R [AGG] > G [GGG] Coding Sequence Variant
macrophage-stimulating protein receptor isoform X9 XP_011532045.1:p.Arg219Gly R (Arg) > G (Gly) Missense Variant
MST1R transcript variant X11 XM_047448165.1:c.655A>G R [AGG] > G [GGG] Coding Sequence Variant
macrophage-stimulating protein receptor isoform X10 XP_047304121.1:p.Arg219Gly R (Arg) > G (Gly) Missense Variant
MST1R transcript variant X12 XM_011533744.3:c.655A>G R [AGG] > G [GGG] Coding Sequence Variant
macrophage-stimulating protein receptor isoform X11 XP_011532046.1:p.Arg219Gly R (Arg) > G (Gly) Missense Variant
MST1R transcript variant X13 XM_047448166.1:c.655A>G R [AGG] > G [GGG] Coding Sequence Variant
macrophage-stimulating protein receptor isoform X12 XP_047304122.1:p.Arg219Gly R (Arg) > G (Gly) Missense Variant
MST1R transcript variant X14 XM_047448167.1:c.655A>G R [AGG] > G [GGG] Coding Sequence Variant
macrophage-stimulating protein receptor isoform X13 XP_047304123.1:p.Arg219Gly R (Arg) > G (Gly) Missense Variant
MST1R transcript variant X15 XM_047448168.1:c.655A>G R [AGG] > G [GGG] Coding Sequence Variant
macrophage-stimulating protein receptor isoform X14 XP_047304124.1:p.Arg219Gly R (Arg) > G (Gly) Missense Variant
MST1R transcript variant X16 XM_047448169.1:c.655A>G R [AGG] > G [GGG] Coding Sequence Variant
macrophage-stimulating protein receptor isoform X15 XP_047304125.1:p.Arg219Gly R (Arg) > G (Gly) Missense Variant
MST1R transcript variant X17 XM_047448170.1:c.655A>G R [AGG] > G [GGG] Coding Sequence Variant
macrophage-stimulating protein receptor isoform X16 XP_047304126.1:p.Arg219Gly R (Arg) > G (Gly) Missense Variant
MST1R transcript variant X18 XM_047448171.1:c.655A>G R [AGG] > G [GGG] Coding Sequence Variant
macrophage-stimulating protein receptor isoform X17 XP_047304127.1:p.Arg219Gly R (Arg) > G (Gly) Missense Variant
MST1R transcript variant X19 XM_047448172.1:c.655A>G R [AGG] > G [GGG] Coding Sequence Variant
macrophage-stimulating protein receptor isoform X18 XP_047304128.1:p.Arg219Gly R (Arg) > G (Gly) Missense Variant
MST1R transcript variant X20 XM_047448173.1:c.655A>G R [AGG] > G [GGG] Coding Sequence Variant
macrophage-stimulating protein receptor isoform X19 XP_047304129.1:p.Arg219Gly R (Arg) > G (Gly) Missense Variant
MST1R transcript variant X21 XM_047448174.1:c.655A>G R [AGG] > G [GGG] Coding Sequence Variant
macrophage-stimulating protein receptor isoform X20 XP_047304130.1:p.Arg219Gly R (Arg) > G (Gly) Missense Variant
MST1R transcript variant X22 XM_047448175.1:c.655A>G R [AGG] > G [GGG] Coding Sequence Variant
macrophage-stimulating protein receptor isoform X21 XP_047304131.1:p.Arg219Gly R (Arg) > G (Gly) Missense Variant
MST1R transcript variant X23 XM_047448176.1:c.655A>G R [AGG] > G [GGG] Coding Sequence Variant
macrophage-stimulating protein receptor isoform X22 XP_047304132.1:p.Arg219Gly R (Arg) > G (Gly) Missense Variant
MST1R transcript variant X24 XM_047448177.1:c.655A>G R [AGG] > G [GGG] Coding Sequence Variant
macrophage-stimulating protein receptor isoform X23 XP_047304133.1:p.Arg219Gly R (Arg) > G (Gly) Missense Variant
MST1R transcript variant X25 XM_047448178.1:c.655A>G R [AGG] > G [GGG] Coding Sequence Variant
macrophage-stimulating protein receptor isoform X24 XP_047304134.1:p.Arg219Gly R (Arg) > G (Gly) Missense Variant
MST1R transcript variant X26 XM_047448179.1:c.655A>G R [AGG] > G [GGG] Coding Sequence Variant
macrophage-stimulating protein receptor isoform X25 XP_047304135.1:p.Arg219Gly R (Arg) > G (Gly) Missense Variant
MST1R transcript variant X27 XM_047448180.1:c.655A>G R [AGG] > G [GGG] Coding Sequence Variant
macrophage-stimulating protein receptor isoform X26 XP_047304136.1:p.Arg219Gly R (Arg) > G (Gly) Missense Variant
MST1R transcript variant X7 XR_001740155.2:n.919A>G N/A Non Coding Transcript Variant
Help

Clinical Significance tab shows a list of clinical significance entries from ClinVar associated with the variation, per allele. Click on the RCV accession (i.e. RCV000001615.2) or Allele ID (i.e. 12274) to access full ClinVar report.

Not Reported in ClinVar
Help

Aliases tab displays HGVS names representing the variant placements and allele changes on genomic, transcript and protein sequences, per allele. HGVS name is an expression for reporting sequence accession and version, sequence type, position, and allele change. The column "Note" can have two values: "diff" means that there is a difference between the reference allele (variation interval) at the placement reported in HGVS name and the reference alleles reported in other HGVS names, and "rev" means that the sequence of this variation interval at the placement reported in HGVS name is in reverse orientation to the sequence(s) of this variation in other HGVS names not labeled as "rev".

Placement T= C
GRCh38.p14 chr 3 NC_000003.12:g.49902955= NC_000003.12:g.49902955T>C
GRCh37.p13 chr 3 NC_000003.11:g.49940388= NC_000003.11:g.49940388T>C
MST1R RefSeqGene NG_030322.1:g.5919= NG_030322.1:g.5919A>G
MST1R transcript variant 1 NM_002447.4:c.655= NM_002447.4:c.655A>G
MST1R transcript variant 1 NM_002447.3:c.655= NM_002447.3:c.655A>G
MST1R transcript variant 1 NM_002447.2:c.655= NM_002447.2:c.655A>G
MST1R transcript variant 2 NM_001244937.3:c.655= NM_001244937.3:c.655A>G
MST1R transcript variant 2 NM_001244937.2:c.655= NM_001244937.2:c.655A>G
MST1R transcript variant 2 NM_001244937.1:c.655= NM_001244937.1:c.655A>G
MST1R transcript variant 4 NR_134919.2:n.919= NR_134919.2:n.919A>G
MST1R transcript variant 4 NR_134919.1:n.683= NR_134919.1:n.683A>G
MST1R transcript variant 3 NM_001318913.2:c.655= NM_001318913.2:c.655A>G
MST1R transcript variant 3 NM_001318913.1:c.655= NM_001318913.1:c.655A>G
MST1R transcript variant X1 XM_005265170.5:c.655= XM_005265170.5:c.655A>G
MST1R transcript variant X1 XM_005265170.4:c.655= XM_005265170.4:c.655A>G
MST1R transcript variant X1 XM_005265170.3:c.655= XM_005265170.3:c.655A>G
MST1R transcript variant X1 XM_005265170.2:c.655= XM_005265170.2:c.655A>G
MST1R transcript variant X1 XM_005265170.1:c.655= XM_005265170.1:c.655A>G
MST1R transcript variant X2 XM_011533739.3:c.655= XM_011533739.3:c.655A>G
MST1R transcript variant X2 XM_011533739.2:c.655= XM_011533739.2:c.655A>G
MST1R transcript variant X2 XM_011533739.1:c.655= XM_011533739.1:c.655A>G
MST1R transcript variant X8 XM_011533742.3:c.655= XM_011533742.3:c.655A>G
MST1R transcript variant X6 XM_011533742.2:c.655= XM_011533742.2:c.655A>G
MST1R transcript variant X5 XM_011533742.1:c.655= XM_011533742.1:c.655A>G
MST1R transcript variant X4 XM_011533740.3:c.655= XM_011533740.3:c.655A>G
MST1R transcript variant X3 XM_011533740.2:c.655= XM_011533740.2:c.655A>G
MST1R transcript variant X3 XM_011533740.1:c.655= XM_011533740.1:c.655A>G
MST1R transcript variant X5 XM_011533741.3:c.655= XM_011533741.3:c.655A>G
MST1R transcript variant X4 XM_011533741.2:c.655= XM_011533741.2:c.655A>G
MST1R transcript variant X4 XM_011533741.1:c.655= XM_011533741.1:c.655A>G
MST1R transcript variant X10 XM_011533743.3:c.655= XM_011533743.3:c.655A>G
MST1R transcript variant X7 XM_011533743.2:c.655= XM_011533743.2:c.655A>G
MST1R transcript variant X6 XM_011533743.1:c.655= XM_011533743.1:c.655A>G
MST1R transcript variant X12 XM_011533744.3:c.655= XM_011533744.3:c.655A>G
MST1R transcript variant X8 XM_011533744.2:c.655= XM_011533744.2:c.655A>G
MST1R transcript variant X7 XM_011533744.1:c.655= XM_011533744.1:c.655A>G
MST1R transcript variant X7 XR_001740155.2:n.919= XR_001740155.2:n.919A>G
MST1R transcript variant X5 XR_001740155.1:n.678= XR_001740155.1:n.678A>G
MST1R transcript variant X3 XM_047448162.1:c.655= XM_047448162.1:c.655A>G
MST1R transcript variant X9 XM_047448164.1:c.655= XM_047448164.1:c.655A>G
MST1R transcript variant X6 XM_047448163.1:c.655= XM_047448163.1:c.655A>G
MST1R transcript variant X13 XM_047448166.1:c.655= XM_047448166.1:c.655A>G
MST1R transcript variant X16 XM_047448169.1:c.655= XM_047448169.1:c.655A>G
MST1R transcript variant X17 XM_047448170.1:c.655= XM_047448170.1:c.655A>G
MST1R transcript variant X11 XM_047448165.1:c.655= XM_047448165.1:c.655A>G
MST1R transcript variant X18 XM_047448171.1:c.655= XM_047448171.1:c.655A>G
MST1R transcript variant X14 XM_047448167.1:c.655= XM_047448167.1:c.655A>G
MST1R transcript variant X15 XM_047448168.1:c.655= XM_047448168.1:c.655A>G
MST1R transcript variant X19 XM_047448172.1:c.655= XM_047448172.1:c.655A>G
MST1R transcript variant X22 XM_047448175.1:c.655= XM_047448175.1:c.655A>G
MST1R transcript variant X20 XM_047448173.1:c.655= XM_047448173.1:c.655A>G
MST1R transcript variant X21 XM_047448174.1:c.655= XM_047448174.1:c.655A>G
MST1R transcript variant X24 XM_047448177.1:c.655= XM_047448177.1:c.655A>G
MST1R transcript variant X23 XM_047448176.1:c.655= XM_047448176.1:c.655A>G
MST1R transcript variant X25 XM_047448178.1:c.655= XM_047448178.1:c.655A>G
MST1R transcript variant X27 XM_047448180.1:c.655= XM_047448180.1:c.655A>G
MST1R transcript variant X26 XM_047448179.1:c.655= XM_047448179.1:c.655A>G
macrophage-stimulating protein receptor isoform 1 preproprotein NP_002438.2:p.Arg219= NP_002438.2:p.Arg219Gly
macrophage-stimulating protein receptor isoform 2 precursor NP_001231866.1:p.Arg219= NP_001231866.1:p.Arg219Gly
macrophage-stimulating protein receptor isoform 3 precursor NP_001305842.1:p.Arg219= NP_001305842.1:p.Arg219Gly
macrophage-stimulating protein receptor isoform X1 XP_005265227.2:p.Arg219= XP_005265227.2:p.Arg219Gly
macrophage-stimulating protein receptor isoform X2 XP_011532041.1:p.Arg219= XP_011532041.1:p.Arg219Gly
macrophage-stimulating protein receptor isoform X7 XP_011532044.1:p.Arg219= XP_011532044.1:p.Arg219Gly
macrophage-stimulating protein receptor isoform X4 XP_011532042.1:p.Arg219= XP_011532042.1:p.Arg219Gly
macrophage-stimulating protein receptor isoform X5 XP_011532043.1:p.Arg219= XP_011532043.1:p.Arg219Gly
macrophage-stimulating protein receptor isoform X9 XP_011532045.1:p.Arg219= XP_011532045.1:p.Arg219Gly
macrophage-stimulating protein receptor isoform X11 XP_011532046.1:p.Arg219= XP_011532046.1:p.Arg219Gly
macrophage-stimulating protein receptor isoform X3 XP_047304118.1:p.Arg219= XP_047304118.1:p.Arg219Gly
macrophage-stimulating protein receptor isoform X8 XP_047304120.1:p.Arg219= XP_047304120.1:p.Arg219Gly
macrophage-stimulating protein receptor isoform X6 XP_047304119.1:p.Arg219= XP_047304119.1:p.Arg219Gly
macrophage-stimulating protein receptor isoform X12 XP_047304122.1:p.Arg219= XP_047304122.1:p.Arg219Gly
macrophage-stimulating protein receptor isoform X15 XP_047304125.1:p.Arg219= XP_047304125.1:p.Arg219Gly
macrophage-stimulating protein receptor isoform X16 XP_047304126.1:p.Arg219= XP_047304126.1:p.Arg219Gly
macrophage-stimulating protein receptor isoform X10 XP_047304121.1:p.Arg219= XP_047304121.1:p.Arg219Gly
macrophage-stimulating protein receptor isoform X17 XP_047304127.1:p.Arg219= XP_047304127.1:p.Arg219Gly
macrophage-stimulating protein receptor isoform X13 XP_047304123.1:p.Arg219= XP_047304123.1:p.Arg219Gly
macrophage-stimulating protein receptor isoform X14 XP_047304124.1:p.Arg219= XP_047304124.1:p.Arg219Gly
macrophage-stimulating protein receptor isoform X18 XP_047304128.1:p.Arg219= XP_047304128.1:p.Arg219Gly
macrophage-stimulating protein receptor isoform X21 XP_047304131.1:p.Arg219= XP_047304131.1:p.Arg219Gly
macrophage-stimulating protein receptor isoform X19 XP_047304129.1:p.Arg219= XP_047304129.1:p.Arg219Gly
macrophage-stimulating protein receptor isoform X20 XP_047304130.1:p.Arg219= XP_047304130.1:p.Arg219Gly
macrophage-stimulating protein receptor isoform X23 XP_047304133.1:p.Arg219= XP_047304133.1:p.Arg219Gly
macrophage-stimulating protein receptor isoform X22 XP_047304132.1:p.Arg219= XP_047304132.1:p.Arg219Gly
macrophage-stimulating protein receptor isoform X24 XP_047304134.1:p.Arg219= XP_047304134.1:p.Arg219Gly
macrophage-stimulating protein receptor isoform X26 XP_047304136.1:p.Arg219= XP_047304136.1:p.Arg219Gly
macrophage-stimulating protein receptor isoform X25 XP_047304135.1:p.Arg219= XP_047304135.1:p.Arg219Gly
macrophage-stimulating protein receptor isoform X1 XP_005265227.1:p.Arg219= XP_005265227.1:p.Arg219Gly
Help

Submissions tab displays variations originally submitted to dbSNP, now supporting this RefSNP cluster (rs). We display Submitter handle, Submission identifier, Date and Build number, when the submission appeared for the first time. Direct submissions to dbSNP have Submission ID in the form of an ss-prefixed number (ss#). Other supporting variations are listed in the table without ss#.

2 SubSNP, 2 Frequency submissions
No Submitter Submission ID Date (Build)
1 EVA_EXAC ss1687018252 Apr 01, 2015 (144)
2 GNOMAD ss2733771167 Nov 08, 2017 (151)
3 ExAC NC_000003.11 - 49940388 Oct 12, 2018 (152)
4 gnomAD - Exomes NC_000003.11 - 49940388 Jul 13, 2019 (153)
Help

History tab displays RefSNPs (Associated ID) from previous builds (Build) that now support the current RefSNP, and the dates, when the history was updated for each Associated ID (History Updated).

Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
6943296, 2850524, ss1687018252, ss2733771167 NC_000003.11:49940387:T:C NC_000003.12:49902954:T:C (self)
Help

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

No publications for rs774465428

Help

The Flanks tab provides retrieving flanking sequences of a SNP on all molecules that have placements.

Genome context:
Select flank length:

Genomic regions, transcripts, and products
Top Help

NCBI Graphical Sequence Viewer display of the genomic region, transcripts and protein products for the reported RefSNP (rs).
Use the zoom option to view the nucleotides around the RefSNP and find other neighboring RefSNPs.
Visit Sequence Viewer for help with navigating inside the display and modifying the selection of displayed data tracks.

Software version is: 2.0.1.post761+d5e8e07