Name: rs7655841
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.

rs7655841

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr4:128969635 (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=0.288232 (76292/264690, TOPMED)
C=0.272688 (38161/139944, GnomAD)
C=0.24340 (6878/28258, 14KJPN) (+ 18 more)
C=0.22489 (5473/24336, ALFA)
C=0.24195 (4055/16760, 8.3KJPN)
C=0.2900 (1857/6404, 1000G_30x)
C=0.2857 (1431/5008, 1000G)
C=0.1185 (531/4480, Estonian)
C=0.1814 (699/3854, ALSPAC)
C=0.1756 (651/3708, TWINSUK)
C=0.1964 (575/2928, KOREAN)
C=0.3072 (580/1888, HapMap)
C=0.2009 (368/1832, Korea1K)
C=0.196 (196/998, GoNL)
C=0.208 (164/788, PRJEB37584)
C=0.157 (94/600, NorthernSweden)
C=0.287 (62/216, Qatari)
C=0.401 (85/212, Vietnamese)
T=0.400 (84/210, SGDP_PRJ)
C=0.12 (5/40, GENOME_DK)
T=0.42 (5/12, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: SCLT1 : 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	24336	T=0.77511	C=0.22489
European	Sub	18112	T=0.83519	C=0.16481
African	Sub	4114	T=0.5265	C=0.4735
African Others	Sub	148	T=0.459	C=0.541
African American	Sub	3966	T=0.5290	C=0.4710
Asian	Sub	124	T=0.694	C=0.306
East Asian	Sub	96	T=0.69	C=0.31
Other Asian	Sub	28	T=0.71	C=0.29
Latin American 1	Sub	168	T=0.780	C=0.220
Latin American 2	Sub	670	T=0.707	C=0.293
South Asian	Sub	98	T=0.89	C=0.11
Other	Sub	1050	T=0.7543	C=0.2457

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=0.711768	C=0.288232
gnomAD - Genomes	Global	Study-wide	139944	T=0.727312	C=0.272688
gnomAD - Genomes	European	Sub	75830	T=0.83202	C=0.16798
gnomAD - Genomes	African	Sub	41902	T=0.52179	C=0.47821
gnomAD - Genomes	American	Sub	13626	T=0.75114	C=0.24886
gnomAD - Genomes	Ashkenazi Jewish	Sub	3320	T=0.8325	C=0.1675
gnomAD - Genomes	East Asian	Sub	3122	T=0.7351	C=0.2649
gnomAD - Genomes	Other	Sub	2144	T=0.7150	C=0.2850
14KJPN	JAPANESE	Study-wide	28258	T=0.75660	C=0.24340
Allele Frequency Aggregator	Total	Global	24336	T=0.77511	C=0.22489
Allele Frequency Aggregator	European	Sub	18112	T=0.83519	C=0.16481
Allele Frequency Aggregator	African	Sub	4114	T=0.5265	C=0.4735
Allele Frequency Aggregator	Other	Sub	1050	T=0.7543	C=0.2457
Allele Frequency Aggregator	Latin American 2	Sub	670	T=0.707	C=0.293
Allele Frequency Aggregator	Latin American 1	Sub	168	T=0.780	C=0.220
Allele Frequency Aggregator	Asian	Sub	124	T=0.694	C=0.306
Allele Frequency Aggregator	South Asian	Sub	98	T=0.89	C=0.11
8.3KJPN	JAPANESE	Study-wide	16760	T=0.75805	C=0.24195
1000Genomes_30x	Global	Study-wide	6404	T=0.7100	C=0.2900
1000Genomes_30x	African	Sub	1786	T=0.4563	C=0.5437
1000Genomes_30x	Europe	Sub	1266	T=0.8183	C=0.1817
1000Genomes_30x	South Asian	Sub	1202	T=0.9251	C=0.0749
1000Genomes_30x	East Asian	Sub	1170	T=0.7256	C=0.2744
1000Genomes_30x	American	Sub	980	T=0.750	C=0.250
1000Genomes	Global	Study-wide	5008	T=0.7143	C=0.2857
1000Genomes	African	Sub	1322	T=0.4592	C=0.5408
1000Genomes	East Asian	Sub	1008	T=0.7192	C=0.2808
1000Genomes	Europe	Sub	1006	T=0.8101	C=0.1899
1000Genomes	South Asian	Sub	978	T=0.927	C=0.073
1000Genomes	American	Sub	694	T=0.754	C=0.246
Genetic variation in the Estonian population	Estonian	Study-wide	4480	T=0.8815	C=0.1185
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.8186	C=0.1814
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.8244	C=0.1756
KOREAN population from KRGDB	KOREAN	Study-wide	2928	T=0.8036	C=0.1964
HapMap	Global	Study-wide	1888	T=0.6928	C=0.3072
HapMap	American	Sub	768	T=0.773	C=0.227
HapMap	African	Sub	690	T=0.552	C=0.448
HapMap	Asian	Sub	254	T=0.772	C=0.228
HapMap	Europe	Sub	176	T=0.778	C=0.222
Korean Genome Project	KOREAN	Study-wide	1832	T=0.7991	C=0.2009
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	T=0.804	C=0.196
CNV burdens in cranial meningiomas	Global	Study-wide	788	T=0.792	C=0.208
CNV burdens in cranial meningiomas	CRM	Sub	788	T=0.792	C=0.208
Northern Sweden	ACPOP	Study-wide	600	T=0.843	C=0.157
Qatari	Global	Study-wide	216	T=0.713	C=0.287
A Vietnamese Genetic Variation Database	Global	Study-wide	212	T=0.599	C=0.401
SGDP_PRJ	Global	Study-wide	210	T=0.400	C=0.600
The Danish reference pan genome	Danish	Study-wide	40	T=0.88	C=0.12
Siberian	Global	Study-wide	12	T=0.42	C=0.58

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.128969635T>C
GRCh37.p13 chr 4	NC_000004.11:g.129890790T>C
SCLT1 RefSeqGene	NG_034202.1:g.128973A>G

Gene: SCLT1, sodium channel and clathrin linker 1 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
SCLT1 transcript variant 1	NM_144643.4:c.777+743A>G	N/A	Intron Variant
SCLT1 transcript variant 2	NM_001300897.2:c.	N/A	Genic Downstream Transcript Variant
SCLT1 transcript variant 3	NM_001300898.2:c.	N/A	Genic Downstream Transcript Variant
SCLT1 transcript variant X1	XM_017007716.3:c.777+743A… XM_017007716.3:c.777+743A>G	N/A	Intron Variant
SCLT1 transcript variant X2	XM_017007717.3:c.777+743A… XM_017007717.3:c.777+743A>G	N/A	Intron Variant
SCLT1 transcript variant X4	XM_017007718.3:c.777+743A… XM_017007718.3:c.777+743A>G	N/A	Intron Variant
SCLT1 transcript variant X6	XM_017007719.2:c.528+743A… XM_017007719.2:c.528+743A>G	N/A	Intron Variant
SCLT1 transcript variant X3	XM_047449590.1:c.777+743A… XM_047449590.1:c.777+743A>G	N/A	Intron Variant
SCLT1 transcript variant X5	XM_047449592.1:c.777+743A… XM_047449592.1:c.777+743A>G	N/A	Intron Variant
SCLT1 transcript variant X7	XM_047449593.1:c.777+743A… XM_047449593.1:c.777+743A>G	N/A	Intron Variant
SCLT1 transcript variant X8	XM_047449594.1:c.777+743A… XM_047449594.1:c.777+743A>G	N/A	Intron Variant
SCLT1 transcript variant X9	XM_047449595.1:c.777+743A… XM_047449595.1:c.777+743A>G	N/A	Intron Variant
SCLT1 transcript variant X9	XM_047449596.1:c.777+743A… XM_047449596.1:c.777+743A>G	N/A	Intron Variant
SCLT1 transcript variant X10	XM_047449597.1:c.777+743A… XM_047449597.1:c.777+743A>G	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	T=	C
GRCh38.p14 chr 4	NC_000004.12:g.128969635=	NC_000004.12:g.128969635T>C
GRCh37.p13 chr 4	NC_000004.11:g.129890790=	NC_000004.11:g.129890790T>C
SCLT1 RefSeqGene	NG_034202.1:g.128973=	NG_034202.1:g.128973A>G
SCLT1 transcript	NM_144643.2:c.777+743=	NM_144643.2:c.777+743A>G
SCLT1 transcript variant 1	NM_144643.4:c.777+743=	NM_144643.4:c.777+743A>G
SCLT1 transcript variant X1	XM_005262732.1:c.-140+743=	XM_005262732.1:c.-140+743A>G
SCLT1 transcript variant X2	XM_005262733.1:c.686+22532=	XM_005262733.1:c.686+22532A>G
SCLT1 transcript variant X1	XM_017007716.3:c.777+743=	XM_017007716.3:c.777+743A>G
SCLT1 transcript variant X2	XM_017007717.3:c.777+743=	XM_017007717.3:c.777+743A>G
SCLT1 transcript variant X4	XM_017007718.3:c.777+743=	XM_017007718.3:c.777+743A>G
SCLT1 transcript variant X6	XM_017007719.2:c.528+743=	XM_017007719.2:c.528+743A>G
SCLT1 transcript variant X3	XM_047449590.1:c.777+743=	XM_047449590.1:c.777+743A>G
SCLT1 transcript variant X5	XM_047449592.1:c.777+743=	XM_047449592.1:c.777+743A>G
SCLT1 transcript variant X7	XM_047449593.1:c.777+743=	XM_047449593.1:c.777+743A>G
SCLT1 transcript variant X8	XM_047449594.1:c.777+743=	XM_047449594.1:c.777+743A>G
SCLT1 transcript variant X9	XM_047449595.1:c.777+743=	XM_047449595.1:c.777+743A>G
SCLT1 transcript variant X9	XM_047449596.1:c.777+743=	XM_047449596.1:c.777+743A>G
SCLT1 transcript variant X10	XM_047449597.1:c.777+743=	XM_047449597.1:c.777+743A>G

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#.

70 SubSNP, 21 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	WI_SSAHASNP	ss11615076	Jul 11, 2003 (116)
2	PERLEGEN	ss23362492	Sep 20, 2004 (123)
3	ILLUMINA	ss65802067	Oct 16, 2006 (127)
4	ILLUMINA	ss74874046	Dec 07, 2007 (129)
5	1000GENOMES	ss108332032	Jan 23, 2009 (130)
6	1000GENOMES	ss110577125	Jan 25, 2009 (130)
7	KRIBB_YJKIM	ss119562809	Dec 01, 2009 (131)
8	COMPLETE_GENOMICS	ss164335069	Jul 04, 2010 (132)
9	ILLUMINA	ss174477782	Jul 04, 2010 (132)
10	BUSHMAN	ss199165687	Jul 04, 2010 (132)
11	1000GENOMES	ss221208426	Jul 14, 2010 (132)
12	1000GENOMES	ss232595788	Jul 14, 2010 (132)
13	1000GENOMES	ss239842883	Jul 15, 2010 (132)
14	BL	ss253513288	May 09, 2011 (134)
15	GMI	ss277926328	May 04, 2012 (137)
16	ILLUMINA	ss537497237	Sep 08, 2015 (146)
17	TISHKOFF	ss557848931	Apr 25, 2013 (138)
18	SSMP	ss651661260	Apr 25, 2013 (138)
19	EVA-GONL	ss980670226	Aug 21, 2014 (142)
20	JMKIDD_LAB	ss1071951978	Aug 21, 2014 (142)
21	1000GENOMES	ss1311786659	Aug 21, 2014 (142)
22	DDI	ss1430047787	Apr 01, 2015 (144)
23	EVA_GENOME_DK	ss1580774004	Apr 01, 2015 (144)
24	EVA_DECODE	ss1590179893	Apr 01, 2015 (144)
25	EVA_UK10K_ALSPAC	ss1611163789	Apr 01, 2015 (144)
26	EVA_UK10K_TWINSUK	ss1654157822	Apr 01, 2015 (144)
27	EVA_SVP	ss1712706469	Apr 01, 2015 (144)
28	HAMMER_LAB	ss1802184513	Sep 08, 2015 (146)
29	WEILL_CORNELL_DGM	ss1923913474	Feb 12, 2016 (147)
30	GENOMED	ss1969866899	Jul 19, 2016 (147)
31	JJLAB	ss2022540838	Sep 14, 2016 (149)
32	USC_VALOUEV	ss2150672050	Dec 20, 2016 (150)
33	HUMAN_LONGEVITY	ss2267096455	Dec 20, 2016 (150)
34	SYSTEMSBIOZJU	ss2625767599	Nov 08, 2017 (151)
35	GRF	ss2706157757	Nov 08, 2017 (151)
36	GNOMAD	ss2815183756	Nov 08, 2017 (151)
37	SWEGEN	ss2995544349	Nov 08, 2017 (151)
38	BIOINF_KMB_FNS_UNIBA	ss3025046913	Nov 08, 2017 (151)
39	CSHL	ss3345958486	Nov 08, 2017 (151)
40	ILLUMINA	ss3629065423	Oct 12, 2018 (152)
41	ILLUMINA	ss3638511782	Oct 12, 2018 (152)
42	ILLUMINA	ss3643461220	Oct 12, 2018 (152)
43	EGCUT_WGS	ss3663451331	Jul 13, 2019 (153)
44	EVA_DECODE	ss3713050641	Jul 13, 2019 (153)
45	ACPOP	ss3731603485	Jul 13, 2019 (153)
46	EVA	ss3762403754	Jul 13, 2019 (153)
47	KHV_HUMAN_GENOMES	ss3805560649	Jul 13, 2019 (153)
48	EVA	ss3828806167	Apr 26, 2020 (154)
49	EVA	ss3837848857	Apr 26, 2020 (154)
50	EVA	ss3843288269	Apr 26, 2020 (154)
51	SGDP_PRJ	ss3860039858	Apr 26, 2020 (154)
52	KRGDB	ss3906350149	Apr 26, 2020 (154)
53	KOGIC	ss3955111089	Apr 26, 2020 (154)
54	EVA	ss3984535019	Apr 26, 2021 (155)
55	EVA	ss4017168683	Apr 26, 2021 (155)
56	TOPMED	ss4631779673	Apr 26, 2021 (155)
57	TOMMO_GENOMICS	ss5167975200	Apr 26, 2021 (155)
58	1000G_HIGH_COVERAGE	ss5260998069	Oct 13, 2022 (156)
59	EVA	ss5352253313	Oct 13, 2022 (156)
60	HUGCELL_USP	ss5459561033	Oct 13, 2022 (156)
61	EVA	ss5507729864	Oct 13, 2022 (156)
62	1000G_HIGH_COVERAGE	ss5543049445	Oct 13, 2022 (156)
63	SANFORD_IMAGENETICS	ss5624567426	Oct 13, 2022 (156)
64	SANFORD_IMAGENETICS	ss5636077200	Oct 13, 2022 (156)
65	TOMMO_GENOMICS	ss5702958841	Oct 13, 2022 (156)
66	YY_MCH	ss5805527986	Oct 13, 2022 (156)
67	EVA	ss5844704448	Oct 13, 2022 (156)
68	EVA	ss5854440470	Oct 13, 2022 (156)
69	EVA	ss5865479197	Oct 13, 2022 (156)
70	EVA	ss5964482856	Oct 13, 2022 (156)
71	1000Genomes	NC_000004.11 - 129890790	Oct 12, 2018 (152)
72	1000Genomes_30x	NC_000004.12 - 128969635	Oct 13, 2022 (156)
73	The Avon Longitudinal Study of Parents and Children	NC_000004.11 - 129890790	Oct 12, 2018 (152)
74	Genetic variation in the Estonian population	NC_000004.11 - 129890790	Oct 12, 2018 (152)
75	The Danish reference pan genome	NC_000004.11 - 129890790	Apr 26, 2020 (154)
76	gnomAD - Genomes	NC_000004.12 - 128969635	Apr 26, 2021 (155)
77	Genome of the Netherlands Release 5	NC_000004.11 - 129890790	Apr 26, 2020 (154)
78	HapMap	NC_000004.12 - 128969635	Apr 26, 2020 (154)
79	KOREAN population from KRGDB	NC_000004.11 - 129890790	Apr 26, 2020 (154)
80	Korean Genome Project	NC_000004.12 - 128969635	Apr 26, 2020 (154)
81	Northern Sweden	NC_000004.11 - 129890790	Jul 13, 2019 (153)
82	CNV burdens in cranial meningiomas	NC_000004.11 - 129890790	Apr 26, 2021 (155)
83	Qatari	NC_000004.11 - 129890790	Apr 26, 2020 (154)
84	SGDP_PRJ	NC_000004.11 - 129890790	Apr 26, 2020 (154)
85	Siberian	NC_000004.11 - 129890790	Apr 26, 2020 (154)
86	8.3KJPN	NC_000004.11 - 129890790	Apr 26, 2021 (155)
87	14KJPN	NC_000004.12 - 128969635	Oct 13, 2022 (156)
88	TopMed	NC_000004.12 - 128969635	Apr 26, 2021 (155)
89	UK 10K study - Twins	NC_000004.11 - 129890790	Oct 12, 2018 (152)
90	A Vietnamese Genetic Variation Database	NC_000004.11 - 129890790	Jul 13, 2019 (153)
91	ALFA	NC_000004.12 - 128969635	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
ss108332032, ss110577125, ss164335069, ss199165687, ss253513288, ss277926328, ss1590179893, ss1712706469, ss3643461220	NC_000004.10:130110239:T:C	NC_000004.12:128969634:T:C	(self)
23260838, 12942699, 9189579, 6938943, 5728377, 13527543, 4888350, 84380, 5955404, 12056838, 3188404, 25944507, 12942699, 2849714, ss221208426, ss232595788, ss239842883, ss537497237, ss557848931, ss651661260, ss980670226, ss1071951978, ss1311786659, ss1430047787, ss1580774004, ss1611163789, ss1654157822, ss1802184513, ss1923913474, ss1969866899, ss2022540838, ss2150672050, ss2625767599, ss2706157757, ss2815183756, ss2995544349, ss3345958486, ss3629065423, ss3638511782, ss3663451331, ss3731603485, ss3762403754, ss3828806167, ss3837848857, ss3860039858, ss3906350149, ss3984535019, ss4017168683, ss5167975200, ss5352253313, ss5507729864, ss5624567426, ss5636077200, ss5844704448, ss5964482856	NC_000004.11:129890789:T:C	NC_000004.12:128969634:T:C	(self)
30575380, 164783026, 2708716, 11489090, 36795945, 469157229, 8970779052, ss2267096455, ss3025046913, ss3713050641, ss3805560649, ss3843288269, ss3955111089, ss4631779673, ss5260998069, ss5459561033, ss5543049445, ss5702958841, ss5805527986, ss5854440470, ss5865479197	NC_000004.12:128969634:T:C	NC_000004.12:128969634:T:C	(self)
ss11615076	NT_016354.15:54385920:T:C	NC_000004.12:128969634:T:C	(self)
ss23362492, ss65802067, ss74874046, ss119562809, ss174477782	NT_016354.19:54438510:T:C	NC_000004.12:128969634: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 rs7655841

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

rs7655841