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dbSNP Short Genetic Variations

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.

rs10424065

Current Build 153

Released July 9, 2019

Organism
Homo sapiens
Position
chr19:3545024 (GRCh38.p12) 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=0.07460 (9367/125568, TOPMED)
T=0.0677 (2117/31272, GnomAD)
T=0.084 (419/5008, 1000G) (+ 4 more)
T=0.005 (22/4480, Estonian)
T=0.008 (31/3854, ALSPAC)
T=0.009 (34/3708, TWINSUK)
T=0.01 (4/600, NorthernSweden)
Clinical Significance
Reported in ClinVar
Gene : Consequence
MFSD12 : Intron Variant
Publications
0 citations
Genomic View
See rs on genome
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.p12 chr 19 NC_000019.10:g.3545024C>T
GRCh37.p13 chr 19 NC_000019.9:g.3545022C>T
Gene: MFSD12, major facilitator superfamily domain containing 12 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
MFSD12 transcript variant 4 NM_001287529.1:c. N/A Intron Variant
MFSD12 transcript variant 3 NM_174983.5:c. N/A Intron Variant
MFSD12 transcript variant X2 XM_005259490.4:c. N/A Intron Variant
MFSD12 transcript variant X1 XM_006722647.3:c. N/A Intron Variant
MFSD12 transcript variant X3 XM_011527684.2:c. N/A Intron Variant
MFSD12 transcript variant X4 XM_017026288.1:c. N/A Intron 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.

Allele: T (allele ID: 485881 )
ClinVar Accession Disease Names Clinical Significance
RCV000584737.1 MFSD12 POLYMORPHISM Benign
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 125568 C=0.92540 T=0.07460
gnomAD - Genomes Global Study-wide 31272 C=0.9323 T=0.0677
gnomAD - Genomes European Sub 18844 C=0.9920 T=0.0080
gnomAD - Genomes African Sub 8650 C=0.778 T=0.222
gnomAD - Genomes East Asian Sub 1552 C=1.000 T=0.000
gnomAD - Genomes Other Sub 1088 C=0.975 T=0.025
gnomAD - Genomes American Sub 848 C=0.99 T=0.01
gnomAD - Genomes Ashkenazi Jewish Sub 290 C=0.97 T=0.03
1000Genomes Global Study-wide 5008 C=0.916 T=0.084
1000Genomes African Sub 1322 C=0.702 T=0.298
1000Genomes East Asian Sub 1008 C=0.999 T=0.001
1000Genomes Europe Sub 1006 C=0.991 T=0.009
1000Genomes South Asian Sub 978 C=1.00 T=0.00
1000Genomes American Sub 694 C=0.98 T=0.02
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.995 T=0.005
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.992 T=0.008
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.991 T=0.009
Northern Sweden ACPOP Study-wide 600 C=0.99 T=0.01
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 Note
GRCh38.p12 chr 19 NC_000019.10:g.3545024= NC_000019.10:g.3545024C>T
GRCh37.p13 chr 19 NC_000019.9:g.3545022= NC_000019.9:g.3545022C>T
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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#.

24 SubSNP, 7 Frequency, 1 ClinVar submissions
No Submitter Submission ID Date (Build)
1 BCM_SSAHASNP ss14725383 Dec 05, 2003 (119)
2 HGSV ss78950965 Dec 07, 2007 (129)
3 1000GENOMES ss114760376 Jan 25, 2009 (130)
4 ILLUMINA-UK ss117621675 Feb 14, 2009 (130)
5 COMPLETE_GENOMICS ss168909203 Jul 04, 2010 (132)
6 1000GENOMES ss228015402 Jul 14, 2010 (132)
7 TISHKOFF ss565818189 Apr 25, 2013 (138)
8 EVA-GONL ss994028269 Aug 21, 2014 (142)
9 1000GENOMES ss1362127075 Aug 21, 2014 (142)
10 EVA_UK10K_ALSPAC ss1637458953 Apr 01, 2015 (144)
11 EVA_UK10K_TWINSUK ss1680452986 Apr 01, 2015 (144)
12 HAMMER_LAB ss1809180295 Sep 08, 2015 (146)
13 WEILL_CORNELL_DGM ss1937506832 Feb 12, 2016 (147)
14 JJLAB ss2029528434 Sep 14, 2016 (149)
15 HUMAN_LONGEVITY ss2223834894 Dec 20, 2016 (150)
16 TOPMED ss2389262077 Dec 20, 2016 (150)
17 GNOMAD ss2959793992 Nov 08, 2017 (151)
18 SWEGEN ss3016991095 Nov 08, 2017 (151)
19 TOPMED ss3286380343 Nov 08, 2017 (151)
20 EGCUT_WGS ss3683837378 Jul 13, 2019 (153)
21 EVA_DECODE ss3702221670 Jul 13, 2019 (153)
22 ACPOP ss3742802005 Jul 13, 2019 (153)
23 EVA ss3755741763 Jul 13, 2019 (153)
24 KHV_HUMAN_GENOMES ss3820996011 Jul 13, 2019 (153)
25 1000Genomes NC_000019.9 - 3545022 Oct 12, 2018 (152)
26 The Avon Longitudinal Study of Parents and Children NC_000019.9 - 3545022 Oct 12, 2018 (152)
27 Genetic variation in the Estonian population NC_000019.9 - 3545022 Oct 12, 2018 (152)
28 gnomAD - Genomes NC_000019.9 - 3545022 Jul 13, 2019 (153)
29 Northern Sweden NC_000019.9 - 3545022 Jul 13, 2019 (153)
30 TopMed NC_000019.10 - 3545024 Oct 12, 2018 (152)
31 UK 10K study - Twins NC_000019.9 - 3545022 Oct 12, 2018 (152)
32 ClinVar RCV000584737.1 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
ss78950965, ss114760376, ss117621675, ss168909203 NC_000019.8:3496021:C:T NC_000019.10:3545023:C:T (self)
75495607, 41841359, 29575626, 206054421, 16086870, 41841359, ss228015402, ss565818189, ss994028269, ss1362127075, ss1637458953, ss1680452986, ss1809180295, ss1937506832, ss2029528434, ss2389262077, ss2959793992, ss3016991095, ss3683837378, ss3742802005, ss3755741763 NC_000019.9:3545021:C:T NC_000019.10:3545023:C:T (self)
RCV000584737.1, 175736608, ss2223834894, ss3286380343, ss3702221670, ss3820996011 NC_000019.10:3545023:C:T NC_000019.10:3545023:C:T (self)
ss14725383 NT_011255.14:3485021:C:T NC_000019.10:3545023: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 rs10424065

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.post104+4a6ee9c