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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.

rs62304360

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr4:54733263 (GRCh38.p13) 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=0.013079 (3462/264690, TOPMED)
T=0.012460 (1746/140134, GnomAD)
T=0.01400 (266/18996, ALFA) (+ 10 more)
T=0.0068 (34/5008, 1000G)
T=0.0145 (65/4480, Estonian)
T=0.0140 (54/3854, ALSPAC)
T=0.0181 (67/3708, TWINSUK)
T=0.007 (7/998, GoNL)
T=0.025 (15/600, NorthernSweden)
T=0.034 (18/534, MGP)
T=0.03 (1/40, GENOME_DK)
C=0.5 (3/6, SGDP_PRJ)
T=0.5 (3/6, SGDP_PRJ)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
KIT : 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.p13 chr 4 NC_000004.12:g.54733263C>T
GRCh37.p13 chr 4 NC_000004.11:g.55599429C>T
KIT RefSeqGene (LRG_307) NG_007456.1:g.80269C>T
Gene: KIT, KIT proto-oncogene, receptor tyrosine kinase (plus strand)
Molecule type Change Amino acid[Codon] SO Term
KIT transcript variant 1 NM_000222.3:c.2484+71C>T N/A Intron Variant
KIT transcript variant 2 NM_001093772.2:c.2472+71C…

NM_001093772.2:c.2472+71C>T

N/A Intron Variant
KIT transcript variant 3 NM_001385284.1:c.2487+71C…

NM_001385284.1:c.2487+71C>T

N/A Intron Variant
KIT transcript variant 4 NM_001385285.1:c.2481+71C…

NM_001385285.1:c.2481+71C>T

N/A Intron Variant
KIT transcript variant 5 NM_001385286.1:c.2469+71C…

NM_001385286.1:c.2469+71C>T

N/A Intron Variant
KIT transcript variant 6 NM_001385288.1:c.2475+71C…

NM_001385288.1:c.2475+71C>T

N/A Intron Variant
KIT transcript variant 7 NM_001385290.1:c.2484+71C…

NM_001385290.1:c.2484+71C>T

N/A Intron Variant
KIT transcript variant 8 NM_001385292.1:c.2472+71C…

NM_001385292.1:c.2472+71C>T

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.

Not Reported in ClinVar

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: 20201027095038
Population Group Sample Size Ref Allele Alt Allele
Total Global 18996 C=0.98600 T=0.01400
European Sub 14370 C=0.98344 T=0.01656
African Sub 2950 C=0.9959 T=0.0041
African Others Sub 114 C=1.000 T=0.000
African American Sub 2836 C=0.9958 T=0.0042
Asian Sub 114 C=1.000 T=0.000
East Asian Sub 88 C=1.00 T=0.00
Other Asian Sub 26 C=1.00 T=0.00
Latin American 1 Sub 146 C=0.973 T=0.027
Latin American 2 Sub 610 C=0.992 T=0.008
South Asian Sub 100 C=1.00 T=0.00
Other Sub 706 C=0.990 T=0.010


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=0.986921 T=0.013079
gnomAD - Genomes Global Study-wide 140134 C=0.987540 T=0.012460
gnomAD - Genomes European Sub 75920 C=0.98483 T=0.01517
gnomAD - Genomes African Sub 42000 C=0.99540 T=0.00460
gnomAD - Genomes American Sub 13616 C=0.98201 T=0.01799
gnomAD - Genomes Ashkenazi Jewish Sub 3324 C=0.9636 T=0.0364
gnomAD - Genomes East Asian Sub 3132 C=0.9997 T=0.0003
gnomAD - Genomes Other Sub 2142 C=0.9841 T=0.0159
1000Genomes Global Study-wide 5008 C=0.9932 T=0.0068
1000Genomes African Sub 1322 C=0.9985 T=0.0015
1000Genomes East Asian Sub 1008 C=1.0000 T=0.0000
1000Genomes Europe Sub 1006 C=0.9831 T=0.0169
1000Genomes South Asian Sub 978 C=0.997 T=0.003
1000Genomes American Sub 694 C=0.983 T=0.017
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.9855 T=0.0145
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.9860 T=0.0140
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.9819 T=0.0181
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 C=0.993 T=0.007
Northern Sweden ACPOP Study-wide 600 C=0.975 T=0.025
Medical Genome Project healthy controls from Spanish population Spanish controls Study-wide 534 C=0.966 T=0.034
The Danish reference pan genome Danish Study-wide 40 C=0.97 T=0.03
SGDP_PRJ Global Study-wide 6 C=0.5 T=0.5
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.p13 chr 4 NC_000004.12:g.54733263= NC_000004.12:g.54733263C>T
GRCh37.p13 chr 4 NC_000004.11:g.55599429= NC_000004.11:g.55599429C>T
KIT RefSeqGene (LRG_307) NG_007456.1:g.80269= NG_007456.1:g.80269C>T
KIT transcript variant 1 NM_000222.2:c.2484+71= NM_000222.2:c.2484+71C>T
KIT transcript variant 1 NM_000222.3:c.2484+71= NM_000222.3:c.2484+71C>T
KIT transcript variant 2 NM_001093772.1:c.2472+71= NM_001093772.1:c.2472+71C>T
KIT transcript variant 2 NM_001093772.2:c.2472+71= NM_001093772.2:c.2472+71C>T
KIT transcript variant 3 NM_001385284.1:c.2487+71= NM_001385284.1:c.2487+71C>T
KIT transcript variant 4 NM_001385285.1:c.2481+71= NM_001385285.1:c.2481+71C>T
KIT transcript variant 5 NM_001385286.1:c.2469+71= NM_001385286.1:c.2469+71C>T
KIT transcript variant 6 NM_001385288.1:c.2475+71= NM_001385288.1:c.2475+71C>T
KIT transcript variant 7 NM_001385290.1:c.2484+71= NM_001385290.1:c.2484+71C>T
KIT transcript variant 8 NM_001385292.1:c.2472+71= NM_001385292.1:c.2472+71C>T
KIT transcript variant X1 XM_005265740.1:c.2487+71= XM_005265740.1:c.2487+71C>T
KIT transcript variant X2 XM_005265741.1:c.2484+71= XM_005265741.1:c.2484+71C>T
KIT transcript variant X3 XM_005265742.1:c.2475+71= XM_005265742.1:c.2475+71C>T
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#.

25 SubSNP, 12 Frequency submissions
No Submitter Submission ID Date (Build)
1 BCMHGSC_JDW ss92584500 Mar 24, 2008 (129)
2 SNP500CANCER ss105437305 Feb 05, 2009 (130)
3 1000GENOMES ss232386663 Jul 14, 2010 (132)
4 EVA-GONL ss980098214 Aug 21, 2014 (142)
5 1000GENOMES ss1309680840 Aug 21, 2014 (142)
6 EVA_GENOME_DK ss1580549156 Apr 01, 2015 (144)
7 EVA_DECODE ss1589595863 Apr 01, 2015 (144)
8 EVA_UK10K_ALSPAC ss1610058181 Apr 01, 2015 (144)
9 EVA_UK10K_TWINSUK ss1653052214 Apr 01, 2015 (144)
10 EVA_MGP ss1711059771 Apr 01, 2015 (144)
11 GENOMED ss1966658492 Feb 12, 2016 (147)
12 JJLAB ss2022252266 Sep 14, 2016 (149)
13 HUMAN_LONGEVITY ss2262838322 Dec 20, 2016 (150)
14 TOPMED ss2430488362 Dec 20, 2016 (150)
15 GNOMAD ss2809155206 Nov 08, 2017 (151)
16 SWEGEN ss2994678256 Nov 08, 2017 (151)
17 TOPMED ss3428733774 Nov 08, 2017 (151)
18 EGCUT_WGS ss3662563336 Jul 13, 2019 (153)
19 EVA_DECODE ss3712025726 Jul 13, 2019 (153)
20 ACPOP ss3731135574 Jul 13, 2019 (153)
21 KHV_HUMAN_GENOMES ss3804915997 Jul 13, 2019 (153)
22 SGDP_PRJ ss3858917370 Apr 26, 2020 (154)
23 EVA ss3986280013 Apr 26, 2021 (155)
24 TOPMED ss4613414304 Apr 26, 2021 (155)
25 CPQ_GEN_INCA ss5236860039 Apr 26, 2021 (155)
26 1000Genomes NC_000004.11 - 55599429 Oct 12, 2018 (152)
27 The Avon Longitudinal Study of Parents and Children NC_000004.11 - 55599429 Oct 12, 2018 (152)
28 Genetic variation in the Estonian population NC_000004.11 - 55599429 Oct 12, 2018 (152)
29 The Danish reference pan genome NC_000004.11 - 55599429 Apr 26, 2020 (154)
30 gnomAD - Genomes NC_000004.12 - 54733263 Apr 26, 2021 (155)
31 Genome of the Netherlands Release 5 NC_000004.11 - 55599429 Apr 26, 2020 (154)
32 Medical Genome Project healthy controls from Spanish population NC_000004.11 - 55599429 Apr 26, 2020 (154)
33 Northern Sweden NC_000004.11 - 55599429 Jul 13, 2019 (153)
34 SGDP_PRJ NC_000004.11 - 55599429 Apr 26, 2020 (154)
35 TopMed NC_000004.12 - 54733263 Apr 26, 2021 (155)
36 UK 10K study - Twins NC_000004.11 - 55599429 Oct 12, 2018 (152)
37 ALFA NC_000004.12 - 54733263 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
ss92584500, ss1589595863 NC_000004.10:55294185:C:T NC_000004.12:54733262:C:T (self)
21073968, 11728686, 8301584, 6714095, 5170759, 175531, 4420439, 10934350, 11728686, ss232386663, ss980098214, ss1309680840, ss1580549156, ss1610058181, ss1653052214, ss1711059771, ss1966658492, ss2022252266, ss2430488362, ss2809155206, ss2994678256, ss3662563336, ss3731135574, ss3858917370, ss3986280013, ss5236860039 NC_000004.11:55599428:C:T NC_000004.12:54733262:C:T (self)
149382080, 281765835, 450791860, 8398133770, ss2262838322, ss3428733774, ss3712025726, ss3804915997, ss4613414304 NC_000004.12:54733262:C:T NC_000004.12:54733262:C:T (self)
ss105437305 NT_022853.15:2939311:C:T NC_000004.12:54733262: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 rs62304360

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.post596+ae089ad