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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.

rs774505948

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr9:127479947 (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
C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.000004 (1/264690, TOPMED)
T=0.000016 (4/251390, GnomAD_exome)
T=0.000017 (2/121098, ExAC) (+ 1 more)
T=0.00006 (2/35432, ALFA)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
LRSAM1 : Missense Variant
Publications
0 citations
Genomic View
See rs on genome

ALFA Allele Frequency
The ALFA project provide aggregate allele frequency from dbGaP. More information is available on the project page including descriptions, data access, and terms of use.

Release Version: 20230706150541
Population Group Sample Size Ref Allele Alt Allele
Total Global 51794 C=0.99994 T=0.00006
European Sub 36678 C=0.99992 T=0.00008
African Sub 7756 C=1.0000 T=0.0000
African Others Sub 298 C=1.000 T=0.000
African American Sub 7458 C=1.0000 T=0.0000
Asian Sub 112 C=1.000 T=0.000
East Asian Sub 86 C=1.00 T=0.00
Other Asian Sub 26 C=1.00 T=0.00
Latin American 1 Sub 500 C=1.000 T=0.000
Latin American 2 Sub 628 C=1.000 T=0.000
South Asian Sub 98 C=1.00 T=0.00
Other Sub 6022 C=1.0000 T=0.0000


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
TopMed Global Study-wide 264690 C=0.999996 T=0.000004
gnomAD - Exomes Global Study-wide 251390 C=0.999984 T=0.000016
gnomAD - Exomes European Sub 135326 C=0.999985 T=0.000015
gnomAD - Exomes Asian Sub 49010 C=0.99996 T=0.00004
gnomAD - Exomes American Sub 34590 C=1.00000 T=0.00000
gnomAD - Exomes African Sub 16250 C=1.00000 T=0.00000
gnomAD - Exomes Ashkenazi Jewish Sub 10080 C=1.00000 T=0.00000
gnomAD - Exomes Other Sub 6134 C=1.0000 T=0.0000
ExAC Global Study-wide 121098 C=0.999983 T=0.000017
ExAC Europe Sub 73118 C=0.99999 T=0.00001
ExAC Asian Sub 25148 C=0.99996 T=0.00004
ExAC American Sub 11568 C=1.00000 T=0.00000
ExAC African Sub 10360 C=1.00000 T=0.00000
ExAC Other Sub 904 C=1.000 T=0.000
Allele Frequency Aggregator Total Global 35432 C=0.99994 T=0.00006
Allele Frequency Aggregator European Sub 26588 C=0.99992 T=0.00008
Allele Frequency Aggregator Other Sub 4588 C=1.0000 T=0.0000
Allele Frequency Aggregator African Sub 2918 C=1.0000 T=0.0000
Allele Frequency Aggregator Latin American 2 Sub 628 C=1.000 T=0.000
Allele Frequency Aggregator Latin American 1 Sub 500 C=1.000 T=0.000
Allele Frequency Aggregator Asian Sub 112 C=1.000 T=0.000
Allele Frequency Aggregator South Asian Sub 98 C=1.00 T=0.00
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 9 NC_000009.12:g.127479947C>T
GRCh37.p13 chr 9 NC_000009.11:g.130242226C>T
LRSAM1 RefSeqGene (LRG_373) NG_032008.1:g.33462C>T
Gene: LRSAM1, leucine rich repeat and sterile alpha motif containing 1 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
LRSAM1 transcript variant 1 NM_138361.5:c.1012C>T R [CGG] > W [TGG] Coding Sequence Variant
E3 ubiquitin-protein ligase LRSAM1 isoform 1 NP_612370.3:p.Arg338Trp R (Arg) > W (Trp) Missense Variant
LRSAM1 transcript variant 4 NM_001190723.3:c.1012C>T R [CGG] > W [TGG] Coding Sequence Variant
E3 ubiquitin-protein ligase LRSAM1 isoform 2 NP_001177652.1:p.Arg338Trp R (Arg) > W (Trp) Missense Variant
LRSAM1 transcript variant 2 NM_001005373.4:c.1012C>T R [CGG] > W [TGG] Coding Sequence Variant
E3 ubiquitin-protein ligase LRSAM1 isoform 1 NP_001005373.1:p.Arg338Trp R (Arg) > W (Trp) Missense Variant
LRSAM1 transcript variant 6 NM_001384143.1:c.1012C>T R [CGG] > W [TGG] Coding Sequence Variant
E3 ubiquitin-protein ligase LRSAM1 isoform 3 NP_001371072.1:p.Arg338Trp R (Arg) > W (Trp) Missense Variant
LRSAM1 transcript variant 5 NM_001384142.1:c.1012C>T R [CGG] > W [TGG] Coding Sequence Variant
E3 ubiquitin-protein ligase LRSAM1 isoform 1 NP_001371071.1:p.Arg338Trp R (Arg) > W (Trp) Missense Variant
LRSAM1 transcript variant 7 NM_001384144.1:c.223C>T R [CGG] > W [TGG] Coding Sequence Variant
E3 ubiquitin-protein ligase LRSAM1 isoform 4 NP_001371073.1:p.Arg75Trp R (Arg) > W (Trp) Missense Variant
LRSAM1 transcript variant 3 NM_001005374.4:c.1012C>T R [CGG] > W [TGG] Coding Sequence Variant
E3 ubiquitin-protein ligase LRSAM1 isoform 1 NP_001005374.1:p.Arg338Trp R (Arg) > W (Trp) Missense Variant
LRSAM1 transcript variant 8 NR_168891.1:n.1360C>T N/A Non Coding Transcript Variant
LRSAM1 transcript variant 9 NR_168892.1:n.1360C>T N/A Non Coding Transcript Variant
LRSAM1 transcript variant X1 XM_047424058.1:c.1012C>T R [CGG] > W [TGG] Coding Sequence Variant
E3 ubiquitin-protein ligase LRSAM1 isoform X1 XP_047280014.1:p.Arg338Trp R (Arg) > W (Trp) Missense Variant
LRSAM1 transcript variant X2 XM_047424059.1:c.223C>T R [CGG] > W [TGG] Coding Sequence Variant
E3 ubiquitin-protein ligase LRSAM1 isoform X2 XP_047280015.1:p.Arg75Trp R (Arg) > W (Trp) Missense 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 C= T
GRCh38.p14 chr 9 NC_000009.12:g.127479947= NC_000009.12:g.127479947C>T
GRCh37.p13 chr 9 NC_000009.11:g.130242226= NC_000009.11:g.130242226C>T
LRSAM1 RefSeqGene (LRG_373) NG_032008.1:g.33462= NG_032008.1:g.33462C>T
LRSAM1 transcript variant 1 NM_138361.5:c.1012= NM_138361.5:c.1012C>T
LRSAM1 transcript variant 2 NM_001005373.4:c.1012= NM_001005373.4:c.1012C>T
LRSAM1 transcript variant 2 NM_001005373.3:c.1012= NM_001005373.3:c.1012C>T
LRSAM1 transcript variant 3 NM_001005374.4:c.1012= NM_001005374.4:c.1012C>T
LRSAM1 transcript variant 3 NM_001005374.3:c.1012= NM_001005374.3:c.1012C>T
LRSAM1 transcript variant 4 NM_001190723.3:c.1012= NM_001190723.3:c.1012C>T
LRSAM1 transcript variant 4 NM_001190723.2:c.1012= NM_001190723.2:c.1012C>T
LRSAM1 transcript variant 5 NM_001384142.1:c.1012= NM_001384142.1:c.1012C>T
LRSAM1 transcript variant 8 NR_168891.1:n.1360= NR_168891.1:n.1360C>T
LRSAM1 transcript variant 9 NR_168892.1:n.1360= NR_168892.1:n.1360C>T
LRSAM1 transcript variant 7 NM_001384144.1:c.223= NM_001384144.1:c.223C>T
LRSAM1 transcript variant 6 NM_001384143.1:c.1012= NM_001384143.1:c.1012C>T
LRSAM1 transcript variant X1 XM_047424058.1:c.1012= XM_047424058.1:c.1012C>T
LRSAM1 transcript variant X2 XM_047424059.1:c.223= XM_047424059.1:c.223C>T
E3 ubiquitin-protein ligase LRSAM1 isoform 1 NP_612370.3:p.Arg338= NP_612370.3:p.Arg338Trp
E3 ubiquitin-protein ligase LRSAM1 isoform 1 NP_001005373.1:p.Arg338= NP_001005373.1:p.Arg338Trp
E3 ubiquitin-protein ligase LRSAM1 isoform 1 NP_001005374.1:p.Arg338= NP_001005374.1:p.Arg338Trp
E3 ubiquitin-protein ligase LRSAM1 isoform 2 NP_001177652.1:p.Arg338= NP_001177652.1:p.Arg338Trp
E3 ubiquitin-protein ligase LRSAM1 isoform 1 NP_001371071.1:p.Arg338= NP_001371071.1:p.Arg338Trp
E3 ubiquitin-protein ligase LRSAM1 isoform 4 NP_001371073.1:p.Arg75= NP_001371073.1:p.Arg75Trp
E3 ubiquitin-protein ligase LRSAM1 isoform 3 NP_001371072.1:p.Arg338= NP_001371072.1:p.Arg338Trp
E3 ubiquitin-protein ligase LRSAM1 isoform X1 XP_047280014.1:p.Arg338= XP_047280014.1:p.Arg338Trp
E3 ubiquitin-protein ligase LRSAM1 isoform X2 XP_047280015.1:p.Arg75= XP_047280015.1:p.Arg75Trp
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#.

4 SubSNP, 4 Frequency submissions
No Submitter Submission ID Date (Build)
1 EVA_EXAC ss1689663742 Apr 01, 2015 (144)
2 GNOMAD ss2737880583 Nov 08, 2017 (151)
3 SWEGEN ss3005632903 Nov 08, 2017 (151)
4 TOPMED ss4836623382 Apr 26, 2021 (155)
5 ExAC NC_000009.11 - 130242226 Oct 12, 2018 (152)
6 gnomAD - Exomes NC_000009.11 - 130242226 Jul 13, 2019 (153)
7 TopMed NC_000009.12 - 127479947 Apr 26, 2021 (155)
8 ALFA NC_000009.12 - 127479947 Apr 26, 2021 (155)
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
9800129, 7069130, ss1689663742, ss2737880583, ss3005632903 NC_000009.11:130242225:C:T NC_000009.12:127479946:C:T (self)
674000943, 14484137099, ss4836623382 NC_000009.12:127479946:C:T NC_000009.12:127479946:C:T (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 rs774505948

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