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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.

rs4253164

Current Build 152

Released October 2, 2018

Organism
Homo sapiens
Position
chr10:49483113 (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
T>G
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.05994 (7526/125568, TOPMED)
G=0.0650 (2011/30958, GnomAD)
G=0.035 (175/5008, 1000G) (+ 3 more)
G=0.114 (511/4480, Estonian)
G=0.088 (338/3854, ALSPAC)
G=0.090 (333/3708, TWINSUK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
ERCC6 : 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 10 NC_000010.11:g.49483113T>G
GRCh37.p13 chr 10 NC_000010.10:g.50691159T>G
ERCC6 RefSeqGene (LRG_465) NG_009442.1:g.60989A>C
Gene: ERCC6, ERCC excision repair 6, chromatin remodeling factor (minus strand)
Molecule type Change Amino acid[Codon] SO Term
ERCC6 transcript variant 3 NM_000124.3:c. N/A Intron Variant
ERCC6 transcript variant 4 NM_001346440.1:c. N/A Intron Variant
ERCC6 transcript variant 1 NM_001277058.1:c. N/A Genic Downstream Transcript Variant
ERCC6 transcript variant 2 NM_001277059.1:c. N/A Genic 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

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 T=0.94006 G=0.05994
gnomAD - Genomes Global Study-wide 30958 T=0.9350 G=0.0650
gnomAD - Genomes European Sub 18486 T=0.9067 G=0.0933
gnomAD - Genomes African Sub 8730 T=0.983 G=0.017
gnomAD - Genomes East Asian Sub 1620 T=1.000 G=0.000
gnomAD - Genomes Other Sub 982 T=0.93 G=0.07
gnomAD - Genomes American Sub 838 T=0.95 G=0.05
gnomAD - Genomes Ashkenazi Jewish Sub 302 T=0.91 G=0.09
1000Genomes Global Study-wide 5008 T=0.965 G=0.035
1000Genomes African Sub 1322 T=0.998 G=0.002
1000Genomes East Asian Sub 1008 T=0.999 G=0.001
1000Genomes Europe Sub 1006 T=0.900 G=0.100
1000Genomes South Asian Sub 978 T=0.96 G=0.04
1000Genomes American Sub 694 T=0.95 G=0.05
Genetic variation in the Estonian population Estonian Study-wide 4480 T=0.886 G=0.114
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.912 G=0.088
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.910 G=0.090
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= G Note
GRCh38.p12 chr 10 NC_000010.11:g.49483113T= NC_000010.11:g.49483113T>G
GRCh37.p13 chr 10 NC_000010.10:g.50691159T= NC_000010.10:g.50691159T>G
ERCC6 RefSeqGene (LRG_465) NG_009442.1:g.60989A= NG_009442.1:g.60989A>C
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, 6 Frequency submissions
No Submitter Submission ID Date (Build)
1 EGP_SNPS ss5609139 Feb 20, 2003 (111)
2 EGP_SNPS ss66861967 Nov 29, 2006 (127)
3 1000GENOMES ss109416228 Jan 24, 2009 (130)
4 COMPLETE_GENOMICS ss174530601 Jul 04, 2010 (132)
5 1000GENOMES ss235163767 Jul 15, 2010 (132)
6 EVA-GONL ss987461294 Aug 21, 2014 (142)
7 JMKIDD_LAB ss1076963846 Aug 21, 2014 (142)
8 1000GENOMES ss1337341777 Aug 21, 2014 (142)
9 EVA_GENOME_DK ss1575095319 Apr 01, 2015 (144)
10 EVA_DECODE ss1597125173 Apr 01, 2015 (144)
11 EVA_UK10K_ALSPAC ss1624520511 Apr 01, 2015 (144)
12 EVA_UK10K_TWINSUK ss1667514544 Apr 01, 2015 (144)
13 WEILL_CORNELL_DGM ss1930819064 Feb 12, 2016 (147)
14 ILLUMINA ss1959261207 Feb 12, 2016 (147)
15 JJLAB ss2026131387 Sep 14, 2016 (149)
16 USC_VALOUEV ss2154405520 Dec 20, 2016 (150)
17 HUMAN_LONGEVITY ss2174586525 Dec 20, 2016 (150)
18 TOPMED ss2337558401 Dec 20, 2016 (150)
19 GNOMAD ss2888506281 Nov 08, 2017 (151)
20 SWEGEN ss3006433280 Nov 08, 2017 (151)
21 ILLUMINA ss3021238561 Nov 08, 2017 (151)
22 TOPMED ss3119242177 Nov 08, 2017 (151)
23 CSHL ss3349107397 Nov 08, 2017 (151)
24 BIOINF_KMB_FNS_UNIBA ss3645136953 Oct 12, 2018 (152)
25 ILLUMINA ss3651591184 Oct 12, 2018 (152)
26 1000Genomes NC_000010.10 - 50691159 Oct 12, 2018 (152)
27 The Avon Longitudinal Study of Parents and Children NC_000010.10 - 50691159 Oct 12, 2018 (152)
28 Genetic variation in the Estonian population NC_000010.10 - 50691159 Oct 12, 2018 (152)
29 gnomAD - Genomes NC_000010.10 - 50691159 Oct 12, 2018 (152)
30 TopMed NC_000010.11 - 49483113 Oct 12, 2018 (152)
31 UK 10K study - Twins NC_000010.10 - 50691159 Oct 12, 2018 (152)
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
ss109416228, ss174530601, ss1597125173 NC_000010.9:50361164:T= NC_000010.11:49483112:T= (self)
49725255, 27602514, 19591512, 22207802, 27602514, ss235163767, ss987461294, ss1076963846, ss1337341777, ss1575095319, ss1624520511, ss1667514544, ss1930819064, ss1959261207, ss2026131387, ss2154405520, ss2337558401, ss2888506281, ss3006433280, ss3021238561, ss3349107397, ss3651591184 NC_000010.10:50691158:T= NC_000010.11:49483112:T= (self)
42182023, ss2174586525, ss3119242177, ss3645136953 NC_000010.11:49483112:T= NC_000010.11:49483112:T= (self)
ss5609139, ss66861967 NT_030059.13:1495622:T= NC_000010.11:49483112:T= (self)
ss109416228, ss174530601, ss1597125173 NC_000010.9:50361164:T>G NC_000010.11:49483112:T>G (self)
49725255, 27602514, 19591512, 22207802, 27602514, ss235163767, ss987461294, ss1076963846, ss1337341777, ss1575095319, ss1624520511, ss1667514544, ss1930819064, ss1959261207, ss2026131387, ss2154405520, ss2337558401, ss2888506281, ss3006433280, ss3021238561, ss3349107397, ss3651591184 NC_000010.10:50691158:T>G NC_000010.11:49483112:T>G (self)
42182023, ss2174586525, ss3119242177, ss3645136953 NC_000010.11:49483112:T>G NC_000010.11:49483112:T>G (self)
ss5609139, ss66861967 NT_030059.13:1495622:T>G NC_000010.11:49483112:T>G (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 rs4253164

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.post63+3f7b20b