Name: rs76971852
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.

rs76971852

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr4:76229502 (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=0.049851 (13195/264690, TOPMED)
T=0.052785 (7400/140192, GnomAD)
T=0.00959 (271/28258, 14KJPN) (+ 17 more)
T=0.06098 (1152/18890, ALFA)
T=0.00931 (156/16760, 8.3KJPN)
T=0.0392 (251/6404, 1000G_30x)
T=0.0405 (203/5008, 1000G)
T=0.0725 (325/4480, Estonian)
T=0.0615 (237/3854, ALSPAC)
T=0.0628 (233/3708, TWINSUK)
T=0.0055 (16/2922, KOREAN)
T=0.0038 (7/1832, Korea1K)
T=0.065 (65/998, GoNL)
T=0.058 (35/600, NorthernSweden)
T=0.069 (15/216, Qatari)
C=0.50 (29/58, SGDP_PRJ)
T=0.50 (29/58, SGDP_PRJ)
T=0.03 (1/40, GENOME_DK)
C=0.5 (4/8, Siberian)
T=0.5 (4/8, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: FAM47E : Intron Variant
SCARB2 : 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	C=0.93902	T=0.06098
European	Sub	14286	C=0.93077	T=0.06923
African	Sub	2946	C=0.9705	T=0.0295
African Others	Sub	114	C=0.965	T=0.035
African American	Sub	2832	C=0.9707	T=0.0293
Asian	Sub	112	C=1.000	T=0.000
East Asian	Sub	86	C=1.00	T=0.00
Other Asian	Sub	26	C=1.00	T=0.00
Latin American 1	Sub	146	C=0.945	T=0.055
Latin American 2	Sub	610	C=0.951	T=0.049
South Asian	Sub	98	C=0.91	T=0.09
Other	Sub	692	C=0.958	T=0.042

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	C=0.950149	T=0.049851
gnomAD - Genomes	Global	Study-wide	140192	C=0.947215	T=0.052785
gnomAD - Genomes	European	Sub	75910	C=0.93314	T=0.06686
gnomAD - Genomes	African	Sub	42032	C=0.96752	T=0.03248
gnomAD - Genomes	American	Sub	13648	C=0.95875	T=0.04125
gnomAD - Genomes	Ashkenazi Jewish	Sub	3320	C=0.9331	T=0.0669
gnomAD - Genomes	East Asian	Sub	3134	C=0.9860	T=0.0140
gnomAD - Genomes	Other	Sub	2148	C=0.9390	T=0.0610
14KJPN	JAPANESE	Study-wide	28258	C=0.99041	T=0.00959
Allele Frequency Aggregator	Total	Global	18890	C=0.93902	T=0.06098
Allele Frequency Aggregator	European	Sub	14286	C=0.93077	T=0.06923
Allele Frequency Aggregator	African	Sub	2946	C=0.9705	T=0.0295
Allele Frequency Aggregator	Other	Sub	692	C=0.958	T=0.042
Allele Frequency Aggregator	Latin American 2	Sub	610	C=0.951	T=0.049
Allele Frequency Aggregator	Latin American 1	Sub	146	C=0.945	T=0.055
Allele Frequency Aggregator	Asian	Sub	112	C=1.000	T=0.000
Allele Frequency Aggregator	South Asian	Sub	98	C=0.91	T=0.09
8.3KJPN	JAPANESE	Study-wide	16760	C=0.99069	T=0.00931
1000Genomes_30x	Global	Study-wide	6404	C=0.9608	T=0.0392
1000Genomes_30x	African	Sub	1786	C=0.9731	T=0.0269
1000Genomes_30x	Europe	Sub	1266	C=0.9258	T=0.0742
1000Genomes_30x	South Asian	Sub	1202	C=0.9409	T=0.0591
1000Genomes_30x	East Asian	Sub	1170	C=0.9889	T=0.0111
1000Genomes_30x	American	Sub	980	C=0.974	T=0.026
1000Genomes	Global	Study-wide	5008	C=0.9595	T=0.0405
1000Genomes	African	Sub	1322	C=0.9705	T=0.0295
1000Genomes	East Asian	Sub	1008	C=0.9891	T=0.0109
1000Genomes	Europe	Sub	1006	C=0.9264	T=0.0736
1000Genomes	South Asian	Sub	978	C=0.938	T=0.062
1000Genomes	American	Sub	694	C=0.974	T=0.026
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.9275	T=0.0725
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.9385	T=0.0615
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.9372	T=0.0628
KOREAN population from KRGDB	KOREAN	Study-wide	2922	C=0.9945	T=0.0055
Korean Genome Project	KOREAN	Study-wide	1832	C=0.9962	T=0.0038
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.935	T=0.065
Northern Sweden	ACPOP	Study-wide	600	C=0.942	T=0.058
Qatari	Global	Study-wide	216	C=0.931	T=0.069
SGDP_PRJ	Global	Study-wide	58	C=0.50	T=0.50
The Danish reference pan genome	Danish	Study-wide	40	C=0.97	T=0.03
Siberian	Global	Study-wide	8	C=0.5	T=0.5

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.76229502C>T
GRCh37.p13 chr 4	NC_000004.11:g.77150655C>T

Gene: FAM47E, family with sequence similarity 47 member E (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
FAM47E transcript variant 2	NM_001242936.1:c.81+11814… NM_001242936.1:c.81+11814C>T	N/A	Intron Variant
FAM47E transcript variant 1	NM_001136570.3:c.	N/A	Genic Upstream Transcript Variant

Gene: SCARB2, scavenger receptor class B member 2 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
SCARB2 transcript variant 2	NM_001204255.2:c.	N/A	Genic Upstream Transcript Variant
SCARB2 transcript variant 1	NM_005506.4:c.	N/A	Genic Upstream Transcript Variant
SCARB2 transcript variant X1	XM_047416429.1:c.-358+480… XM_047416429.1:c.-358+4801G>A	N/A	Intron Variant
SCARB2 transcript variant X2	XM_047416430.1:c.	N/A	Genic Upstream 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	C=	T
GRCh38.p14 chr 4	NC_000004.12:g.76229502=	NC_000004.12:g.76229502C>T
GRCh37.p13 chr 4	NC_000004.11:g.77150655=	NC_000004.11:g.77150655C>T
FAM47E transcript variant 2	NM_001242936.1:c.81+11814=	NM_001242936.1:c.81+11814C>T
SCARB2 transcript variant X1	XM_047416429.1:c.-358+4801=	XM_047416429.1:c.-358+4801G>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#.

46 SubSNP, 18 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	ENSEMBL	ss161572711	Dec 01, 2009 (131)
2	COMPLETE_GENOMICS	ss166771661	Jul 04, 2010 (132)
3	1000GENOMES	ss221009765	Jul 14, 2010 (132)
4	1000GENOMES	ss232452947	Jul 14, 2010 (132)
5	SSMP	ss651423152	Apr 25, 2013 (138)
6	EVA-GONL	ss980275865	Aug 21, 2014 (142)
7	JMKIDD_LAB	ss1071659879	Aug 21, 2014 (142)
8	1000GENOMES	ss1310344540	Aug 21, 2014 (142)
9	DDI	ss1429932313	Apr 01, 2015 (144)
10	EVA_GENOME_DK	ss1580621767	Apr 01, 2015 (144)
11	EVA_DECODE	ss1589775142	Apr 01, 2015 (144)
12	EVA_UK10K_ALSPAC	ss1610394472	Apr 01, 2015 (144)
13	EVA_UK10K_TWINSUK	ss1653388505	Apr 01, 2015 (144)
14	WEILL_CORNELL_DGM	ss1923518627	Feb 12, 2016 (147)
15	JJLAB	ss2022345218	Sep 14, 2016 (149)
16	USC_VALOUEV	ss2150473702	Dec 20, 2016 (150)
17	HUMAN_LONGEVITY	ss2264086362	Dec 20, 2016 (150)
18	GNOMAD	ss2811026151	Nov 08, 2017 (151)
19	SWEGEN	ss2994948647	Nov 08, 2017 (151)
20	BIOINF_KMB_FNS_UNIBA	ss3024947201	Nov 08, 2017 (151)
21	CSHL	ss3345789443	Nov 08, 2017 (151)
22	EGCUT_WGS	ss3662831800	Jul 13, 2019 (153)
23	EVA_DECODE	ss3712344373	Jul 13, 2019 (153)
24	ACPOP	ss3731283703	Jul 13, 2019 (153)
25	EVA	ss3761980202	Jul 13, 2019 (153)
26	PACBIO	ss3784760041	Jul 13, 2019 (153)
27	PACBIO	ss3790211727	Jul 13, 2019 (153)
28	PACBIO	ss3795087074	Jul 13, 2019 (153)
29	KHV_HUMAN_GENOMES	ss3805122012	Jul 13, 2019 (153)
30	EVA	ss3828621091	Apr 26, 2020 (154)
31	SGDP_PRJ	ss3859274862	Apr 26, 2020 (154)
32	KRGDB	ss3905533268	Apr 26, 2020 (154)
33	KOGIC	ss3954454127	Apr 26, 2020 (154)
34	TOPMED	ss4619036348	Apr 26, 2021 (155)
35	TOMMO_GENOMICS	ss5166380892	Apr 26, 2021 (155)
36	1000G_HIGH_COVERAGE	ss5259731112	Oct 13, 2022 (156)
37	EVA	ss5349960508	Oct 13, 2022 (156)
38	HUGCELL_USP	ss5458431966	Oct 13, 2022 (156)
39	EVA	ss5507576981	Oct 13, 2022 (156)
40	1000G_HIGH_COVERAGE	ss5541099805	Oct 13, 2022 (156)
41	SANFORD_IMAGENETICS	ss5635342833	Oct 13, 2022 (156)
42	TOMMO_GENOMICS	ss5700912295	Oct 13, 2022 (156)
43	YY_MCH	ss5805218945	Oct 13, 2022 (156)
44	EVA	ss5844202505	Oct 13, 2022 (156)
45	EVA	ss5864041842	Oct 13, 2022 (156)
46	EVA	ss5963720475	Oct 13, 2022 (156)
47	1000Genomes	NC_000004.11 - 77150655	Oct 12, 2018 (152)
48	1000Genomes_30x	NC_000004.12 - 76229502	Oct 13, 2022 (156)
49	The Avon Longitudinal Study of Parents and Children	NC_000004.11 - 77150655	Oct 12, 2018 (152)
50	Genetic variation in the Estonian population	NC_000004.11 - 77150655	Oct 12, 2018 (152)
51	The Danish reference pan genome	NC_000004.11 - 77150655	Apr 26, 2020 (154)
52	gnomAD - Genomes	NC_000004.12 - 76229502	Apr 26, 2021 (155)
53	Genome of the Netherlands Release 5	NC_000004.11 - 77150655	Apr 26, 2020 (154)
54	KOREAN population from KRGDB	NC_000004.11 - 77150655	Apr 26, 2020 (154)
55	Korean Genome Project	NC_000004.12 - 76229502	Apr 26, 2020 (154)
56	Northern Sweden	NC_000004.11 - 77150655	Jul 13, 2019 (153)
57	Qatari	NC_000004.11 - 77150655	Apr 26, 2020 (154)
58	SGDP_PRJ	NC_000004.11 - 77150655	Apr 26, 2020 (154)
59	Siberian	NC_000004.11 - 77150655	Apr 26, 2020 (154)
60	8.3KJPN	NC_000004.11 - 77150655	Apr 26, 2021 (155)
61	14KJPN	NC_000004.12 - 76229502	Oct 13, 2022 (156)
62	TopMed	NC_000004.12 - 76229502	Apr 26, 2021 (155)
63	UK 10K study - Twins	NC_000004.11 - 77150655	Oct 12, 2018 (152)
64	ALFA	NC_000004.12 - 76229502	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
ss166771661, ss1589775142	NC_000004.10:77369678:C:T	NC_000004.12:76229501:C:T	(self)
21761793, 12097132, 8570048, 6786706, 5343516, 12710662, 4568568, 5560557, 11291842, 2990056, 24350199, 12097132, ss221009765, ss232452947, ss651423152, ss980275865, ss1071659879, ss1310344540, ss1429932313, ss1580621767, ss1610394472, ss1653388505, ss1923518627, ss2022345218, ss2150473702, ss2811026151, ss2994948647, ss3345789443, ss3662831800, ss3731283703, ss3761980202, ss3784760041, ss3790211727, ss3795087074, ss3828621091, ss3859274862, ss3905533268, ss5166380892, ss5349960508, ss5507576981, ss5635342833, ss5844202505, ss5963720475	NC_000004.11:77150654:C:T	NC_000004.12:76229501:C:T	(self)
28625740, 154156085, 10832128, 34749399, 456413904, 11734474774, ss2264086362, ss3024947201, ss3712344373, ss3805122012, ss3954454127, ss4619036348, ss5259731112, ss5458431966, ss5541099805, ss5700912295, ss5805218945, ss5864041842	NC_000004.12:76229501:C:T	NC_000004.12:76229501:C:T	(self)
ss161572711	NT_016354.19:1698375:C:T	NC_000004.12:76229501:C:T	(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 rs76971852

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
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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

rs76971852