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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.

rs370670524

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr15:43599282 (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=0.000121 (32/264690, TOPMED)
T=0.000092 (23/251296, GnomAD_exome)
T=0.000179 (25/139932, GnomAD) (+ 3 more)
T=0.000049 (6/121382, ExAC)
T=0.00030 (7/23408, ALFA)
T=0.00008 (1/12994, GO-ESP)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
CKMT1B : Non Coding Transcript Variant
STRC : 500B Downstream 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 23408 C=0.99970 T=0.00030
European Sub 15886 C=0.99962 T=0.00038
African Sub 3540 C=1.0000 T=0.0000
African Others Sub 122 C=1.000 T=0.000
African American Sub 3418 C=1.0000 T=0.0000
Asian Sub 168 C=1.000 T=0.000
East Asian Sub 112 C=1.000 T=0.000
Other Asian Sub 56 C=1.00 T=0.00
Latin American 1 Sub 146 C=1.000 T=0.000
Latin American 2 Sub 610 C=1.000 T=0.000
South Asian Sub 98 C=1.00 T=0.00
Other Sub 2960 C=0.9997 T=0.0003


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=0.999879 T=0.000121
gnomAD - Exomes Global Study-wide 251296 C=0.999908 T=0.000092
gnomAD - Exomes European Sub 135254 C=0.999852 T=0.000148
gnomAD - Exomes Asian Sub 49002 C=0.99998 T=0.00002
gnomAD - Exomes American Sub 34580 C=0.99994 T=0.00006
gnomAD - Exomes African Sub 16254 C=1.00000 T=0.00000
gnomAD - Exomes Ashkenazi Jewish Sub 10076 C=1.00000 T=0.00000
gnomAD - Exomes Other Sub 6130 C=1.0000 T=0.0000
gnomAD - Genomes Global Study-wide 139932 C=0.999821 T=0.000179
gnomAD - Genomes European Sub 75834 C=0.99976 T=0.00024
gnomAD - Genomes African Sub 41872 C=0.99986 T=0.00014
gnomAD - Genomes American Sub 13630 C=1.00000 T=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3320 C=1.0000 T=0.0000
gnomAD - Genomes East Asian Sub 3132 C=1.0000 T=0.0000
gnomAD - Genomes Other Sub 2144 C=0.9995 T=0.0005
ExAC Global Study-wide 121382 C=0.999951 T=0.000049
ExAC Europe Sub 73334 C=0.99995 T=0.00005
ExAC Asian Sub 25160 C=0.99996 T=0.00004
ExAC American Sub 11578 C=1.00000 T=0.00000
ExAC African Sub 10402 C=1.00000 T=0.00000
ExAC Other Sub 908 C=0.999 T=0.001
Allele Frequency Aggregator Total Global 23408 C=0.99970 T=0.00030
Allele Frequency Aggregator European Sub 15886 C=0.99962 T=0.00038
Allele Frequency Aggregator African Sub 3540 C=1.0000 T=0.0000
Allele Frequency Aggregator Other Sub 2960 C=0.9997 T=0.0003
Allele Frequency Aggregator Latin American 2 Sub 610 C=1.000 T=0.000
Allele Frequency Aggregator Asian Sub 168 C=1.000 T=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 C=1.000 T=0.000
Allele Frequency Aggregator South Asian Sub 98 C=1.00 T=0.00
GO Exome Sequencing Project Global Study-wide 12994 C=0.99992 T=0.00008
GO Exome Sequencing Project European American Sub 8594 C=0.9999 T=0.0001
GO Exome Sequencing Project African American Sub 4400 C=1.0000 T=0.0000
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 15 NC_000015.10:g.43599282C>T
GRCh37.p13 chr 15 NC_000015.9:g.43891480C>T
STRC RefSeqGene NG_011636.1:g.24519G>A
Gene: CKMT1B, creatine kinase, mitochondrial 1B (plus strand)
Molecule type Change Amino acid[Codon] SO Term
CKMT1B transcript variant 2 NM_001375484.1:c.*9= N/A 3 Prime UTR Variant
CKMT1B transcript variant 1 NM_020990.5:c.*9= N/A 3 Prime UTR Variant
CKMT1B transcript variant 7 NR_135748.1:n.2718C>T N/A Non Coding Transcript Variant
CKMT1B transcript variant 3 NR_135749.1:n.2698C>T N/A Non Coding Transcript Variant
CKMT1B transcript variant 5 NR_135751.1:n.2558C>T N/A Non Coding Transcript Variant
CKMT1B transcript variant 6 NR_135752.1:n.2325C>T N/A Non Coding Transcript Variant
CKMT1B transcript variant 4 NR_135750.2:n.2669C>T N/A Non Coding Transcript Variant
CKMT1B transcript variant X1 XM_011521194.2:c.*9= N/A 3 Prime UTR Variant
CKMT1B transcript variant X2 XM_011521195.3:c.*9= N/A 3 Prime UTR Variant
CKMT1B transcript variant X3 XM_011521196.2:c.*9= N/A 3 Prime UTR Variant
CKMT1B transcript variant X4 XM_047432132.1:c.*9= N/A 3 Prime UTR Variant
CKMT1B transcript variant X5 XM_047432133.1:c.*9= N/A 3 Prime UTR Variant
CKMT1B transcript variant X6 XM_005254150.5:c.*9= N/A 3 Prime UTR Variant
CKMT1B transcript variant X7 XM_047432134.1:c. N/A Genic Downstream Transcript Variant
Gene: STRC, stereocilin (minus strand) : 500B Downstream Variant
Molecule type Change Amino acid[Codon] SO Term
STRC transcript NM_153700.2:c. N/A Downstream 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 C= T
GRCh38.p14 chr 15 NC_000015.10:g.43599282= NC_000015.10:g.43599282C>T
GRCh37.p13 chr 15 NC_000015.9:g.43891480= NC_000015.9:g.43891480C>T
STRC RefSeqGene NG_011636.1:g.24519= NG_011636.1:g.24519G>A
CKMT1B transcript variant 1 NM_020990.5:c.*9= NM_020990.5:c.*9C>T
CKMT1B transcript variant 1 NM_020990.4:c.*9= NM_020990.4:c.*9C>T
CKMT1B transcript NM_020990.3:c.*9= NM_020990.3:c.*9C>T
CKMT1B transcript variant X6 XM_005254150.5:c.*9= XM_005254150.5:c.*9C>T
CKMT1B transcript variant X6 XM_005254150.4:c.*9= XM_005254150.4:c.*9C>T
CKMT1B transcript variant X6 XM_005254150.3:c.*9= XM_005254150.3:c.*9C>T
CKMT1B transcript variant X3 XM_005254150.2:c.*9= XM_005254150.2:c.*9C>T
CKMT1B transcript variant X3 XM_005254150.1:c.*9= XM_005254150.1:c.*9C>T
CKMT1B transcript variant X2 XM_011521195.3:c.*9= XM_011521195.3:c.*9C>T
CKMT1B transcript variant X2 XM_011521195.2:c.*9= XM_011521195.2:c.*9C>T
CKMT1B transcript variant X2 XM_011521195.1:c.*9= XM_011521195.1:c.*9C>T
CKMT1B transcript variant 4 NR_135750.2:n.2669= NR_135750.2:n.2669C>T
CKMT1B transcript variant 4 NR_135750.1:n.2669= NR_135750.1:n.2669C>T
CKMT1B transcript variant X1 XM_011521194.2:c.*9= XM_011521194.2:c.*9C>T
CKMT1B transcript variant X1 XM_011521194.1:c.*9= XM_011521194.1:c.*9C>T
CKMT1B transcript variant X3 XM_011521196.2:c.*9= XM_011521196.2:c.*9C>T
CKMT1B transcript variant X3 XM_011521196.1:c.*9= XM_011521196.1:c.*9C>T
CKMT1B transcript variant 7 NR_135748.1:n.2718= NR_135748.1:n.2718C>T
CKMT1B transcript variant 3 NR_135749.1:n.2698= NR_135749.1:n.2698C>T
CKMT1B transcript variant 5 NR_135751.1:n.2558= NR_135751.1:n.2558C>T
CKMT1B transcript variant 6 NR_135752.1:n.2325= NR_135752.1:n.2325C>T
CKMT1B transcript variant X4 XM_047432132.1:c.*9= XM_047432132.1:c.*9C>T
CKMT1B transcript variant X5 XM_047432133.1:c.*9= XM_047432133.1:c.*9C>T
CKMT1B transcript variant 2 NM_001375484.1:c.*9= NM_001375484.1:c.*9C>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#.

7 SubSNP, 6 Frequency submissions
No Submitter Submission ID Date (Build)
1 NHLBI-ESP ss713227019 Apr 25, 2013 (138)
2 EVA_EXAC ss1691799948 Apr 01, 2015 (144)
3 GNOMAD ss2741200345 Nov 08, 2017 (151)
4 GNOMAD ss2749291805 Nov 08, 2017 (151)
5 GNOMAD ss2934236461 Nov 08, 2017 (151)
6 EVA ss3824913708 Apr 27, 2020 (154)
7 TOPMED ss4989330957 Apr 26, 2021 (155)
8 ExAC NC_000015.9 - 43891480 Oct 12, 2018 (152)
9 gnomAD - Genomes NC_000015.10 - 43599282 Apr 26, 2021 (155)
10 gnomAD - Exomes NC_000015.9 - 43891480 Jul 13, 2019 (153)
11 GO Exome Sequencing Project NC_000015.9 - 43891480 Oct 12, 2018 (152)
12 TopMed NC_000015.10 - 43599282 Apr 26, 2021 (155)
13 ALFA NC_000015.10 - 43599282 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
2171227, 10464711, 1370980, ss713227019, ss1691799948, ss2741200345, ss2749291805, ss2934236461, ss3824913708 NC_000015.9:43891479:C:T NC_000015.10:43599281:C:T (self)
467367532, 204876617, 125018022, ss4989330957 NC_000015.10:43599281:C:T NC_000015.10:43599281: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 rs370670524

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