Name: rs548960
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.

rs548960

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:29167507 (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=0.193286 (51161/264690, TOPMED)
T=0.198999 (27898/140192, GnomAD)
T=0.04491 (1269/28258, 14KJPN) (+ 16 more)
T=0.22880 (4322/18890, ALFA)
T=0.04391 (736/16760, 8.3KJPN)
T=0.1291 (827/6404, 1000G_30x)
T=0.1280 (641/5008, 1000G)
T=0.2179 (976/4480, Estonian)
T=0.2831 (1091/3854, ALSPAC)
T=0.3023 (1121/3708, TWINSUK)
T=0.0664 (194/2922, KOREAN)
T=0.267 (266/998, GoNL)
T=0.252 (151/600, NorthernSweden)
T=0.269 (58/216, Qatari)
T=0.099 (21/212, Vietnamese)
C=0.434 (59/136, SGDP_PRJ)
T=0.20 (8/40, GENOME_DK)
C=0.50 (6/12, Siberian)
T=0.50 (6/12, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: SRSF4 : Intron Variant
MECR : 500B Downstream 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=0.77120	T=0.22880
European	Sub	14286	C=0.73548	T=0.26452
African	Sub	2946	C=0.9158	T=0.0842
African Others	Sub	114	C=0.956	T=0.044
African American	Sub	2832	C=0.9142	T=0.0858
Asian	Sub	112	C=0.946	T=0.054
East Asian	Sub	86	C=0.94	T=0.06
Other Asian	Sub	26	C=0.96	T=0.04
Latin American 1	Sub	146	C=0.788	T=0.212
Latin American 2	Sub	610	C=0.857	T=0.143
South Asian	Sub	98	C=0.82	T=0.18
Other	Sub	692	C=0.779	T=0.221

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=0.806714	T=0.193286
gnomAD - Genomes	Global	Study-wide	140192	C=0.801001	T=0.198999
gnomAD - Genomes	European	Sub	75900	C=0.73158	T=0.26842
gnomAD - Genomes	African	Sub	42036	C=0.91041	T=0.08959
gnomAD - Genomes	American	Sub	13654	C=0.83280	T=0.16720
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	C=0.7575	T=0.2425
gnomAD - Genomes	East Asian	Sub	3130	C=0.9201	T=0.0799
gnomAD - Genomes	Other	Sub	2148	C=0.8045	T=0.1955
14KJPN	JAPANESE	Study-wide	28258	C=0.95509	T=0.04491
Allele Frequency Aggregator	Total	Global	18890	C=0.77120	T=0.22880
Allele Frequency Aggregator	European	Sub	14286	C=0.73548	T=0.26452
Allele Frequency Aggregator	African	Sub	2946	C=0.9158	T=0.0842
Allele Frequency Aggregator	Other	Sub	692	C=0.779	T=0.221
Allele Frequency Aggregator	Latin American 2	Sub	610	C=0.857	T=0.143
Allele Frequency Aggregator	Latin American 1	Sub	146	C=0.788	T=0.212
Allele Frequency Aggregator	Asian	Sub	112	C=0.946	T=0.054
Allele Frequency Aggregator	South Asian	Sub	98	C=0.82	T=0.18
8.3KJPN	JAPANESE	Study-wide	16760	C=0.95609	T=0.04391
1000Genomes_30x	Global	Study-wide	6404	C=0.8709	T=0.1291
1000Genomes_30x	African	Sub	1786	C=0.9306	T=0.0694
1000Genomes_30x	Europe	Sub	1266	C=0.7385	T=0.2615
1000Genomes_30x	South Asian	Sub	1202	C=0.8810	T=0.1190
1000Genomes_30x	East Asian	Sub	1170	C=0.9316	T=0.0684
1000Genomes_30x	American	Sub	980	C=0.848	T=0.152
1000Genomes	Global	Study-wide	5008	C=0.8720	T=0.1280
1000Genomes	African	Sub	1322	C=0.9289	T=0.0711
1000Genomes	East Asian	Sub	1008	C=0.9266	T=0.0734
1000Genomes	Europe	Sub	1006	C=0.7485	T=0.2515
1000Genomes	South Asian	Sub	978	C=0.880	T=0.120
1000Genomes	American	Sub	694	C=0.852	T=0.148
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.7821	T=0.2179
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.7169	T=0.2831
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.6977	T=0.3023
KOREAN population from KRGDB	KOREAN	Study-wide	2922	C=0.9336	T=0.0664
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.733	T=0.267
Northern Sweden	ACPOP	Study-wide	600	C=0.748	T=0.252
Qatari	Global	Study-wide	216	C=0.731	T=0.269
A Vietnamese Genetic Variation Database	Global	Study-wide	212	C=0.901	T=0.099
SGDP_PRJ	Global	Study-wide	136	C=0.434	T=0.566
The Danish reference pan genome	Danish	Study-wide	40	C=0.80	T=0.20
Siberian	Global	Study-wide	12	C=0.50	T=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.29167507C>T
GRCh37.p13 chr 1	NC_000001.10:g.29494019C>T

Gene: SRSF4, serine and arginine rich splicing factor 4 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
SRSF4 transcript	NM_005626.5:c.108-6990G>A	N/A	Intron Variant
SRSF4 transcript variant X3	XM_011541951.4:c.108-6990… XM_011541951.4:c.108-6990G>A	N/A	Intron Variant
SRSF4 transcript variant X2	XM_047427708.1:c.-593-595… XM_047427708.1:c.-593-595G>A	N/A	Intron Variant
SRSF4 transcript variant X1	XM_047427706.1:c.-1188=	N/A	5 Prime UTR Variant
SRSF4 transcript variant X4	XM_047427714.1:c.	N/A	Genic Upstream Transcript Variant

Gene: MECR, mitochondrial trans-2-enoyl-CoA reductase (minus strand) : 500B Downstream Variant

Molecule type	Change	Amino acid[Codon]	SO Term
MECR transcript variant 2	NM_001024732.4:c.	N/A	N/A
MECR transcript variant 3	NM_001349711.2:c.	N/A	N/A
MECR transcript variant 4	NM_001349712.2:c.	N/A	N/A
MECR transcript variant 5	NM_001349713.2:c.	N/A	N/A
MECR transcript variant 6	NM_001349714.2:c.	N/A	N/A
MECR transcript variant 7	NM_001349715.2:c.	N/A	N/A
MECR transcript variant 8	NM_001349716.2:c.	N/A	N/A
MECR transcript variant 9	NM_001349717.2:c.	N/A	N/A
MECR transcript variant 1	NM_016011.5:c.	N/A	N/A
MECR transcript variant 10	NR_146212.2:n.	N/A	N/A
MECR transcript variant 11	NR_146213.2:n.	N/A	N/A
MECR transcript variant 12	NR_146214.2:n.	N/A	N/A
MECR transcript variant 13	NR_146215.2:n.	N/A	N/A
MECR transcript variant X1	XM_011541539.2:c.	N/A	N/A
MECR transcript variant X2	XM_011541540.3:c.	N/A	N/A
MECR transcript variant X6	XM_011541541.2:c.	N/A	N/A
MECR transcript variant X7	XM_011541546.2:c.	N/A	N/A
MECR transcript variant X8	XM_047422042.1:c.	N/A	N/A
MECR transcript variant X9	XM_047422051.1:c.	N/A	N/A
MECR transcript variant X10	XM_047422055.1:c.	N/A	N/A
MECR transcript variant X3	XR_007060747.1:n.	N/A	Downstream Transcript Variant
MECR transcript variant X5	XR_007060748.1:n.	N/A	Downstream Transcript Variant
MECR transcript variant X4	XR_946663.3:n.	N/A	N/A

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 1	NC_000001.11:g.29167507=	NC_000001.11:g.29167507C>T
GRCh37.p13 chr 1	NC_000001.10:g.29494019=	NC_000001.10:g.29494019C>T
SRSF4 transcript variant X1	XM_047427706.1:c.-1188=	XM_047427706.1:c.-1188G>A
SRSF4 transcript	NM_005626.4:c.108-6990=	NM_005626.4:c.108-6990G>A
SRSF4 transcript	NM_005626.5:c.108-6990=	NM_005626.5:c.108-6990G>A
SRSF4 transcript variant X3	XM_011541951.4:c.108-6990=	XM_011541951.4:c.108-6990G>A
SRSF4 transcript variant X2	XM_047427708.1:c.-593-595=	XM_047427708.1:c.-593-595G>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#.

59 SubSNP, 18 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SC_JCM	ss719861	Aug 11, 2000 (83)
2	KWOK	ss1616847	Oct 18, 2000 (87)
3	KWOK	ss1645486	Oct 18, 2000 (87)
4	KWOK	ss1651196	Oct 18, 2000 (87)
5	KWOK	ss1655386	Oct 18, 2000 (87)
6	TSC-CSHL	ss2913620	Jan 22, 2001 (92)
7	SC_SNP	ss13003975	Dec 05, 2003 (119)
8	ABI	ss41321276	Mar 14, 2006 (126)
9	BCMHGSC_JDW	ss87324437	Mar 23, 2008 (129)
10	BGI	ss102730170	Dec 01, 2009 (131)
11	GMI	ss154808579	Dec 01, 2009 (131)
12	ENSEMBL	ss161244124	Dec 01, 2009 (131)
13	COMPLETE_GENOMICS	ss164027004	Jul 04, 2010 (132)
14	COMPLETE_GENOMICS	ss166290127	Jul 04, 2010 (132)
15	GMI	ss275765126	May 04, 2012 (137)
16	PJP	ss290796454	May 09, 2011 (134)
17	1000GENOMES	ss328500497	May 09, 2011 (134)
18	TISHKOFF	ss553930680	Apr 25, 2013 (138)
19	SSMP	ss647665772	Apr 25, 2013 (138)
20	EVA-GONL	ss974984366	Aug 21, 2014 (142)
21	JMKIDD_LAB	ss1067759520	Aug 21, 2014 (142)
22	1000GENOMES	ss1290190096	Aug 21, 2014 (142)
23	EVA_GENOME_DK	ss1573961059	Apr 01, 2015 (144)
24	EVA_DECODE	ss1584343908	Apr 01, 2015 (144)
25	EVA_UK10K_ALSPAC	ss1599805597	Apr 01, 2015 (144)
26	EVA_UK10K_TWINSUK	ss1642799630	Apr 01, 2015 (144)
27	WEILL_CORNELL_DGM	ss1918195821	Feb 12, 2016 (147)
28	JJLAB	ss2019609103	Sep 14, 2016 (149)
29	USC_VALOUEV	ss2147617146	Dec 20, 2016 (150)
30	HUMAN_LONGEVITY	ss2161046579	Dec 20, 2016 (150)
31	GRF	ss2697522626	Nov 08, 2017 (151)
32	GNOMAD	ss2753134469	Nov 08, 2017 (151)
33	SWEGEN	ss2986531886	Nov 08, 2017 (151)
34	BIOINF_KMB_FNS_UNIBA	ss3023569600	Nov 08, 2017 (151)
35	CSHL	ss3343382359	Nov 08, 2017 (151)
36	EGCUT_WGS	ss3654594678	Jul 12, 2019 (153)
37	EVA_DECODE	ss3686425020	Jul 12, 2019 (153)
38	ACPOP	ss3726900172	Jul 12, 2019 (153)
39	EVA	ss3745985290	Jul 12, 2019 (153)
40	KHV_HUMAN_GENOMES	ss3799004440	Jul 12, 2019 (153)
41	EVA	ss3826089425	Apr 25, 2020 (154)
42	EVA	ss3836432168	Apr 25, 2020 (154)
43	EVA	ss3841837163	Apr 25, 2020 (154)
44	SGDP_PRJ	ss3848489423	Apr 25, 2020 (154)
45	KRGDB	ss3893426515	Apr 25, 2020 (154)
46	TOPMED	ss4443521923	Apr 25, 2021 (155)
47	TOMMO_GENOMICS	ss5143125297	Apr 25, 2021 (155)
48	1000G_HIGH_COVERAGE	ss5241651726	Oct 17, 2022 (156)
49	HUGCELL_USP	ss5442784103	Oct 17, 2022 (156)
50	EVA	ss5505798883	Oct 17, 2022 (156)
51	1000G_HIGH_COVERAGE	ss5513625995	Oct 17, 2022 (156)
52	SANFORD_IMAGENETICS	ss5625187418	Oct 17, 2022 (156)
53	TOMMO_GENOMICS	ss5667633131	Oct 17, 2022 (156)
54	YY_MCH	ss5800444129	Oct 17, 2022 (156)
55	EVA	ss5831723121	Oct 17, 2022 (156)
56	EVA	ss5848836372	Oct 17, 2022 (156)
57	EVA	ss5907551934	Oct 17, 2022 (156)
58	EVA	ss5937003570	Oct 17, 2022 (156)
59	EVA	ss5979946672	Oct 17, 2022 (156)
60	1000Genomes	NC_000001.10 - 29494019	Oct 11, 2018 (152)
61	1000Genomes_30x	NC_000001.11 - 29167507	Oct 17, 2022 (156)
62	The Avon Longitudinal Study of Parents and Children	NC_000001.10 - 29494019	Oct 11, 2018 (152)
63	Genetic variation in the Estonian population	NC_000001.10 - 29494019	Oct 11, 2018 (152)
64	The Danish reference pan genome	NC_000001.10 - 29494019	Apr 25, 2020 (154)
65	gnomAD - Genomes	NC_000001.11 - 29167507	Apr 25, 2021 (155)
66	Genome of the Netherlands Release 5	NC_000001.10 - 29494019	Apr 25, 2020 (154)
67	KOREAN population from KRGDB	NC_000001.10 - 29494019	Apr 25, 2020 (154)
68	Northern Sweden	NC_000001.10 - 29494019	Jul 12, 2019 (153)
69	Qatari	NC_000001.10 - 29494019	Apr 25, 2020 (154)
70	SGDP_PRJ	NC_000001.10 - 29494019	Apr 25, 2020 (154)
71	Siberian	NC_000001.10 - 29494019	Apr 25, 2020 (154)
72	8.3KJPN	NC_000001.10 - 29494019	Apr 25, 2021 (155)
73	14KJPN	NC_000001.11 - 29167507	Oct 17, 2022 (156)
74	TopMed	NC_000001.11 - 29167507	Apr 25, 2021 (155)
75	UK 10K study - Twins	NC_000001.10 - 29494019	Oct 11, 2018 (152)
76	A Vietnamese Genetic Variation Database	NC_000001.10 - 29494019	Jul 12, 2019 (153)
77	ALFA	NC_000001.11 - 29167507	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).

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss87324437, ss164027004, ss166290127, ss275765126, ss290796454, ss1584343908	NC_000001.9:29366605:C:T	NC_000001.11:29167506:C:T	(self)
883869, 471280, 332926, 1438712, 202171, 603909, 185037, 237751, 506403, 133500, 1094604, 471280, 96560, ss328500497, ss553930680, ss647665772, ss974984366, ss1067759520, ss1290190096, ss1573961059, ss1599805597, ss1642799630, ss1918195821, ss2019609103, ss2147617146, ss2697522626, ss2753134469, ss2986531886, ss3343382359, ss3654594678, ss3726900172, ss3745985290, ss3826089425, ss3836432168, ss3848489423, ss3893426515, ss5143125297, ss5505798883, ss5625187418, ss5831723121, ss5937003570, ss5979946672	NC_000001.10:29494018:C:T	NC_000001.11:29167506:C:T	(self)
1151930, 6241719, 1470235, 7128258, 5754312556, ss2161046579, ss3023569600, ss3686425020, ss3799004440, ss3841837163, ss4443521923, ss5241651726, ss5442784103, ss5513625995, ss5667633131, ss5800444129, ss5848836372, ss5907551934	NC_000001.11:29167506:C:T	NC_000001.11:29167506:C:T	(self)
ss13003975	NT_004538.14:686974:C:T	NC_000001.11:29167506:C:T	(self)
ss719861, ss1616847, ss1645486, ss1651196, ss1655386, ss2913620, ss41321276, ss102730170, ss154808579, ss161244124	NT_004610.19:16174106:C:T	NC_000001.11:29167506: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 rs548960

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

rs548960