Name: rs76165594
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.

rs76165594

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:103250 (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: G>A
Variation Type: SNV Single Nucleotide Variation
Frequency: A=0.135645 (15537/114542, GnomAD)
A=0.00899 (254/28258, 14KJPN)
A=0.01062 (178/16760, 8.3KJPN) (+ 6 more)
A=0.19003 (3102/16324, ALFA)
A=0.1287 (824/6404, 1000G_30x)
A=0.0133 (39/2922, KOREAN)
A=0.0136 (25/1832, Korea1K)
G=0.50 (49/98, SGDP_PRJ)
A=0.50 (49/98, SGDP_PRJ)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: LOC124903816 : 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	16324	G=0.80997	A=0.19003
European	Sub	12072	G=0.76806	A=0.23194
African	Sub	2816	G=0.9524	A=0.0476
African Others	Sub	108	G=0.991	A=0.009
African American	Sub	2708	G=0.9509	A=0.0491
Asian	Sub	108	G=1.000	A=0.000
East Asian	Sub	84	G=1.00	A=0.00
Other Asian	Sub	24	G=1.00	A=0.00
Latin American 1	Sub	146	G=0.890	A=0.110
Latin American 2	Sub	610	G=0.880	A=0.120
South Asian	Sub	94	G=0.80	A=0.20
Other	Sub	478	G=0.874	A=0.126

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
gnomAD - Genomes	Global	Study-wide	114542	G=0.864355	A=0.135645
gnomAD - Genomes	European	Sub	58334	G=0.79023	A=0.20977
gnomAD - Genomes	African	Sub	38472	G=0.96730	A=0.03270
gnomAD - Genomes	American	Sub	10384	G=0.88280	A=0.11720
gnomAD - Genomes	East Asian	Sub	3070	G=0.9980	A=0.0020
gnomAD - Genomes	Ashkenazi Jewish	Sub	2554	G=0.7537	A=0.2463
gnomAD - Genomes	Other	Sub	1728	G=0.8900	A=0.1100
14KJPN	JAPANESE	Study-wide	28258	G=0.99101	A=0.00899
8.3KJPN	JAPANESE	Study-wide	16760	G=0.98938	A=0.01062
Allele Frequency Aggregator	Total	Global	16324	G=0.80997	A=0.19003
Allele Frequency Aggregator	European	Sub	12072	G=0.76806	A=0.23194
Allele Frequency Aggregator	African	Sub	2816	G=0.9524	A=0.0476
Allele Frequency Aggregator	Latin American 2	Sub	610	G=0.880	A=0.120
Allele Frequency Aggregator	Other	Sub	478	G=0.874	A=0.126
Allele Frequency Aggregator	Latin American 1	Sub	146	G=0.890	A=0.110
Allele Frequency Aggregator	Asian	Sub	108	G=1.000	A=0.000
Allele Frequency Aggregator	South Asian	Sub	94	G=0.80	A=0.20
1000Genomes_30x	Global	Study-wide	6404	G=0.8713	A=0.1287
1000Genomes_30x	African	Sub	1786	G=0.9821	A=0.0179
1000Genomes_30x	Europe	Sub	1266	G=0.7409	A=0.2591
1000Genomes_30x	South Asian	Sub	1202	G=0.7745	A=0.2255
1000Genomes_30x	East Asian	Sub	1170	G=0.9812	A=0.0188
1000Genomes_30x	American	Sub	980	G=0.826	A=0.174
KOREAN population from KRGDB	KOREAN	Study-wide	2922	G=0.9867	A=0.0133
Korean Genome Project	KOREAN	Study-wide	1832	G=0.9864	A=0.0136
SGDP_PRJ	Global	Study-wide	98	G=0.50	A=0.50

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 1	NC_000001.11:g.103250G>A
GRCh37.p13 chr 1	NC_000001.10:g.103250G>A

Gene: LOC124903816, uncharacterized LOC124903816 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LOC124903816 transcript variant X1	XR_007065337.1:n.	N/A	Intron Variant
LOC124903816 transcript variant X2	XR_007065338.1:n.	N/A	Intron 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	G=	A
GRCh38.p14 chr 1	NC_000001.11:g.103250=	NC_000001.11:g.103250G>A
GRCh37.p13 chr 1	NC_000001.10:g.103250=	NC_000001.10:g.103250G>A

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#.

16 SubSNP, 8 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	ENSEMBL	ss142847966	Dec 01, 2009 (131)
2	PADH-LAB_SPU	ss1713846954	Sep 08, 2015 (147)
3	JJLAB	ss2019497648	Sep 14, 2016 (149)
4	GNOMAD	ss2750608435	Nov 08, 2017 (151)
5	SWEGEN	ss2986142841	Nov 08, 2017 (151)
6	SGDP_PRJ	ss3847985432	Apr 25, 2020 (154)
7	KRGDB	ss3892825234	Apr 25, 2020 (154)
8	KOGIC	ss3943623578	Apr 25, 2020 (154)
9	TOMMO_GENOMICS	ss5142035496	Apr 25, 2021 (155)
10	1000G_HIGH_COVERAGE	ss5240855847	Oct 12, 2022 (156)
11	EVA	ss5316173264	Oct 12, 2022 (156)
12	1000G_HIGH_COVERAGE	ss5512477169	Oct 12, 2022 (156)
13	SANFORD_IMAGENETICS	ss5624743496	Oct 12, 2022 (156)
14	TOMMO_GENOMICS	ss5666168714	Oct 12, 2022 (156)
15	YY_MCH	ss5800240929	Oct 12, 2022 (156)
16	EVA	ss5831416908	Oct 12, 2022 (156)
17	1000Genomes_30x	NC_000001.11 - 103250	Oct 12, 2022 (156)
18	gnomAD - Genomes	NC_000001.11 - 103250	Apr 25, 2021 (155)
19	KOREAN population from KRGDB	NC_000001.10 - 103250	Apr 25, 2020 (154)
20	Korean Genome Project	NC_000001.11 - 103250	Apr 25, 2020 (154)
21	SGDP_PRJ	NC_000001.10 - 103250	Apr 25, 2020 (154)
22	8.3KJPN	NC_000001.10 - 103250	Apr 25, 2021 (155)
23	14KJPN	NC_000001.11 - 103250	Oct 12, 2022 (156)
24	ALFA	NC_000001.11 - 103250	Apr 25, 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).

Associated ID	History Updated (Build)
rs796779951	Jul 19, 2016 (147)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
2628, 2412, 4803, ss1713846954, ss2019497648, ss2750608435, ss2986142841, ss3847985432, ss3892825234, ss5142035496, ss5316173264, ss5624743496, ss5831416908	NC_000001.10:103249:G:A	NC_000001.11:103249:G:A	(self)
3104, 12954, 1579, 5818, 5361216634, ss3943623578, ss5240855847, ss5512477169, ss5666168714, ss5800240929	NC_000001.11:103249:G:A	NC_000001.11:103249:G:A	(self)
ss142847966	NT_077402.2:93249:G:A	NC_000001.11:103249:G:A	(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 rs76165594

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.

Choose placement

dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs76165594