Name: rs76223274
Published: September 21, 2022
License: Open Access

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.

rs76223274

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr4:89716288 (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: T>C
Variation Type: SNV Single Nucleotide Variation
Frequency: C=0.045680 (12091/264690, TOPMED)
C=0.043006 (6026/140120, GnomAD)
C=0.02663 (503/18890, ALFA) (+ 8 more)
C=0.0455 (228/5008, 1000G)
C=0.0004 (2/4480, Estonian)
C=0.0044 (17/3854, ALSPAC)
C=0.0049 (18/3708, TWINSUK)
C=0.0003 (1/2922, KOREAN)
C=0.003 (3/998, GoNL)
C=0.148 (32/216, Qatari)
T=0.35 (9/26, SGDP_PRJ)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: LOC124900602 : Intron 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	18890	T=0.97337	C=0.02663
European	Sub	14286	T=0.99440	C=0.00560
African	Sub	2946	T=0.8734	C=0.1266
African Others	Sub	114	T=0.886	C=0.114
African American	Sub	2832	T=0.8729	C=0.1271
Asian	Sub	112	T=1.000	C=0.000
East Asian	Sub	86	T=1.00	C=0.00
Other Asian	Sub	26	T=1.00	C=0.00
Latin American 1	Sub	146	T=0.918	C=0.082
Latin American 2	Sub	610	T=0.982	C=0.018
South Asian	Sub	98	T=1.00	C=0.00
Other	Sub	692	T=0.961	C=0.039

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").

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Study	Population	Group	Sample Size	Ref Allele	Alt Allele
TopMed	Global	Study-wide	264690	T=0.954320	C=0.045680
gnomAD - Genomes	Global	Study-wide	140120	T=0.956994	C=0.043006
gnomAD - Genomes	European	Sub	75924	T=0.99426	C=0.00574
gnomAD - Genomes	African	Sub	41960	T=0.87800	C=0.12200
gnomAD - Genomes	American	Sub	13632	T=0.98019	C=0.01981
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	T=0.9696	C=0.0304
gnomAD - Genomes	East Asian	Sub	3126	T=0.9997	C=0.0003
gnomAD - Genomes	Other	Sub	2154	T=0.9540	C=0.0460
Allele Frequency Aggregator	Total	Global	18890	T=0.97337	C=0.02663
Allele Frequency Aggregator	European	Sub	14286	T=0.99440	C=0.00560
Allele Frequency Aggregator	African	Sub	2946	T=0.8734	C=0.1266
Allele Frequency Aggregator	Other	Sub	692	T=0.961	C=0.039
Allele Frequency Aggregator	Latin American 2	Sub	610	T=0.982	C=0.018
Allele Frequency Aggregator	Latin American 1	Sub	146	T=0.918	C=0.082
Allele Frequency Aggregator	Asian	Sub	112	T=1.000	C=0.000
Allele Frequency Aggregator	South Asian	Sub	98	T=1.00	C=0.00
1000Genomes	Global	Study-wide	5008	T=0.9545	C=0.0455
1000Genomes	African	Sub	1322	T=0.8502	C=0.1498
1000Genomes	East Asian	Sub	1008	T=1.0000	C=0.0000
1000Genomes	Europe	Sub	1006	T=0.9911	C=0.0089
1000Genomes	South Asian	Sub	978	T=0.992	C=0.008
1000Genomes	American	Sub	694	T=0.981	C=0.019
Genetic variation in the Estonian population	Estonian	Study-wide	4480	T=0.9996	C=0.0004
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.9956	C=0.0044
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.9951	C=0.0049
KOREAN population from KRGDB	KOREAN	Study-wide	2922	T=0.9997	C=0.0003
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	T=0.997	C=0.003
Qatari	Global	Study-wide	216	T=0.852	C=0.148
SGDP_PRJ	Global	Study-wide	26	T=0.35	C=0.65

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 4	NC_000004.12:g.89716288T>C
GRCh37.p13 chr 4	NC_000004.11:g.90637439T>C

Gene: LOC124900602, uncharacterized LOC124900602 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LOC124900602 transcript variant X2	XR_007058466.1:n.	N/A	Intron Variant
LOC124900602 transcript variant X1	XR_001741764.2:n.	N/A	Genic Downstream Transcript Variant
LOC124900602 transcript variant X4	XR_007058465.1:n.	N/A	Genic Downstream Transcript Variant
LOC124900602 transcript variant X3	XR_938983.2:n.	N/A	Genic Downstream Transcript Variant

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

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=	C
GRCh38.p14 chr 4	NC_000004.12:g.89716288=	NC_000004.12:g.89716288T>C
GRCh37.p13 chr 4	NC_000004.11:g.90637439=	NC_000004.11:g.90637439T>C

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#.

29 SubSNP, 11 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	1000GENOMES	ss221062450	Jul 14, 2010 (132)
2	TISHKOFF	ss557678833	Apr 25, 2013 (138)
3	EVA-GONL	ss980374680	Aug 21, 2014 (142)
4	JMKIDD_LAB	ss1071733123	Aug 21, 2014 (142)
5	1000GENOMES	ss1310711431	Aug 21, 2014 (142)
6	DDI	ss1429962034	Apr 01, 2015 (144)
7	EVA_DECODE	ss1589877026	Apr 01, 2015 (144)
8	EVA_UK10K_ALSPAC	ss1610593943	Apr 01, 2015 (144)
9	EVA_UK10K_TWINSUK	ss1653587976	Apr 01, 2015 (144)
10	WEILL_CORNELL_DGM	ss1923618806	Feb 12, 2016 (147)
11	JJLAB	ss2022394410	Sep 14, 2016 (149)
12	HUMAN_LONGEVITY	ss2264853584	Dec 20, 2016 (150)
13	GNOMAD	ss2812075454	Nov 08, 2017 (151)
14	AFFY	ss2985921925	Nov 08, 2017 (151)
15	SWEGEN	ss2995098831	Nov 08, 2017 (151)
16	EGCUT_WGS	ss3662986591	Jul 13, 2019 (153)
17	EVA_DECODE	ss3712525006	Jul 13, 2019 (153)
18	KHV_HUMAN_GENOMES	ss3805236119	Jul 13, 2019 (153)
19	EVA	ss3828669885	Apr 26, 2020 (154)
20	SGDP_PRJ	ss3859469631	Apr 26, 2020 (154)
21	KRGDB	ss3905740879	Apr 26, 2020 (154)
22	TOPMED	ss4622232082	Apr 26, 2021 (155)
23	EVA	ss5350543286	Oct 13, 2022 (156)
24	HUGCELL_USP	ss5458720746	Oct 13, 2022 (156)
25	EVA	ss5507612776	Oct 13, 2022 (156)
26	SANFORD_IMAGENETICS	ss5635529240	Oct 13, 2022 (156)
27	EVA	ss5844329675	Oct 13, 2022 (156)
28	EVA	ss5864411302	Oct 13, 2022 (156)
29	EVA	ss5963913988	Oct 13, 2022 (156)
30	1000Genomes	NC_000004.11 - 90637439	Oct 12, 2018 (152)
31	The Avon Longitudinal Study of Parents and Children	NC_000004.11 - 90637439	Oct 12, 2018 (152)
32	Genetic variation in the Estonian population	NC_000004.11 - 90637439	Oct 12, 2018 (152)
33	gnomAD - Genomes	NC_000004.12 - 89716288	Apr 26, 2021 (155)
34	Genome of the Netherlands Release 5	NC_000004.11 - 90637439	Apr 26, 2020 (154)
35	KOREAN population from KRGDB	NC_000004.11 - 90637439	Apr 26, 2020 (154)
36	Qatari	NC_000004.11 - 90637439	Apr 26, 2020 (154)
37	SGDP_PRJ	NC_000004.11 - 90637439	Apr 26, 2020 (154)
38	TopMed	NC_000004.12 - 89716288	Apr 26, 2021 (155)
39	UK 10K study - Twins	NC_000004.11 - 90637439	Oct 12, 2018 (152)
40	ALFA	NC_000004.12 - 89716288	Apr 26, 2021 (155)

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
ss1589877026	NC_000004.10:90856461:T:C	NC_000004.12:89716287:T:C	(self)
22143177, 12316530, 8724839, 5439811, 12918273, 5660736, 11486611, 12316530, ss221062450, ss557678833, ss980374680, ss1071733123, ss1310711431, ss1429962034, ss1610593943, ss1653587976, ss1923618806, ss2022394410, ss2812075454, ss2985921925, ss2995098831, ss3662986591, ss3828669885, ss3859469631, ss3905740879, ss5350543286, ss5507612776, ss5635529240, ss5844329675, ss5963913988	NC_000004.11:90637438:T:C	NC_000004.12:89716287:T:C	(self)
156830013, 459609638, 320574778, ss2264853584, ss3712525006, ss3805236119, ss4622232082, ss5458720746, ss5864411302	NC_000004.12:89716287:T:C	NC_000004.12:89716287:T:C	(self)

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

No publications for rs76223274

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.

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dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs76223274