Name: rs4768258
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.

rs4768258

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr12:40420782 (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=0.039019 (10328/264690, TOPMED)
A=0.029181 (4086/140024, GnomAD)
A=0.02849 (1188/41692, ALFA) (+ 17 more)
A=0.03465 (979/28258, 14KJPN)
A=0.03556 (596/16760, 8.3KJPN)
A=0.0568 (364/6404, 1000G_30x)
A=0.0595 (298/5008, 1000G)
A=0.0246 (110/4480, Estonian)
A=0.0176 (68/3854, ALSPAC)
A=0.0183 (68/3708, TWINSUK)
A=0.0329 (96/2922, KOREAN)
A=0.020 (20/998, GoNL)
A=0.017 (10/600, NorthernSweden)
A=0.009 (2/234, HapMap)
A=0.102 (22/216, Qatari)
A=0.062 (13/210, Vietnamese)
G=0.44 (37/84, SGDP_PRJ)
A=0.03 (1/40, GENOME_DK)
G=0.5 (4/8, Siberian)
A=0.5 (4/8, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: MUC19 : Intron Variant
LOC105369736 : 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	41692	G=0.97151	A=0.02849
European	Sub	33778	G=0.97330	A=0.02670
African	Sub	2946	G=0.9946	A=0.0054
African Others	Sub	114	G=0.991	A=0.009
African American	Sub	2832	G=0.9947	A=0.0053
Asian	Sub	112	G=0.964	A=0.036
East Asian	Sub	86	G=0.97	A=0.03
Other Asian	Sub	26	G=0.96	A=0.04
Latin American 1	Sub	146	G=0.938	A=0.062
Latin American 2	Sub	610	G=0.797	A=0.203
South Asian	Sub	98	G=0.82	A=0.18
Other	Sub	4002	G=0.9713	A=0.0287

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	G=0.960981	A=0.039019
gnomAD - Genomes	Global	Study-wide	140024	G=0.970819	A=0.029181
gnomAD - Genomes	European	Sub	75802	G=0.97695	A=0.02305
gnomAD - Genomes	African	Sub	41986	G=0.99178	A=0.00822
gnomAD - Genomes	American	Sub	13636	G=0.88237	A=0.11763
gnomAD - Genomes	Ashkenazi Jewish	Sub	3320	G=0.9437	A=0.0563
gnomAD - Genomes	East Asian	Sub	3132	G=0.9655	A=0.0345
gnomAD - Genomes	Other	Sub	2148	G=0.9558	A=0.0442
Allele Frequency Aggregator	Total	Global	41692	G=0.97151	A=0.02849
Allele Frequency Aggregator	European	Sub	33778	G=0.97330	A=0.02670
Allele Frequency Aggregator	Other	Sub	4002	G=0.9713	A=0.0287
Allele Frequency Aggregator	African	Sub	2946	G=0.9946	A=0.0054
Allele Frequency Aggregator	Latin American 2	Sub	610	G=0.797	A=0.203
Allele Frequency Aggregator	Latin American 1	Sub	146	G=0.938	A=0.062
Allele Frequency Aggregator	Asian	Sub	112	G=0.964	A=0.036
Allele Frequency Aggregator	South Asian	Sub	98	G=0.82	A=0.18
14KJPN	JAPANESE	Study-wide	28258	G=0.96535	A=0.03465
8.3KJPN	JAPANESE	Study-wide	16760	G=0.96444	A=0.03556
1000Genomes_30x	Global	Study-wide	6404	G=0.9432	A=0.0568
1000Genomes_30x	African	Sub	1786	G=0.9978	A=0.0022
1000Genomes_30x	Europe	Sub	1266	G=0.9771	A=0.0229
1000Genomes_30x	South Asian	Sub	1202	G=0.9043	A=0.0957
1000Genomes_30x	East Asian	Sub	1170	G=0.9402	A=0.0598
1000Genomes_30x	American	Sub	980	G=0.851	A=0.149
1000Genomes	Global	Study-wide	5008	G=0.9405	A=0.0595
1000Genomes	African	Sub	1322	G=0.9970	A=0.0030
1000Genomes	East Asian	Sub	1008	G=0.9395	A=0.0605
1000Genomes	Europe	Sub	1006	G=0.9771	A=0.0229
1000Genomes	South Asian	Sub	978	G=0.896	A=0.104
1000Genomes	American	Sub	694	G=0.844	A=0.156
Genetic variation in the Estonian population	Estonian	Study-wide	4480	G=0.9754	A=0.0246
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.9824	A=0.0176
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.9817	A=0.0183
KOREAN population from KRGDB	KOREAN	Study-wide	2922	G=0.9671	A=0.0329
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	G=0.980	A=0.020
Northern Sweden	ACPOP	Study-wide	600	G=0.983	A=0.017
HapMap	Global	Study-wide	234	G=0.991	A=0.009
HapMap	American	Sub	120	G=0.983	A=0.017
HapMap	African	Sub	114	G=1.000	A=0.000
Qatari	Global	Study-wide	216	G=0.898	A=0.102
A Vietnamese Genetic Variation Database	Global	Study-wide	210	G=0.938	A=0.062
SGDP_PRJ	Global	Study-wide	84	G=0.44	A=0.56
The Danish reference pan genome	Danish	Study-wide	40	G=0.97	A=0.03
Siberian	Global	Study-wide	8	G=0.5	A=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 12	NC_000012.12:g.40420782G>A
GRCh37.p13 chr 12	NC_000012.11:g.40814584G>A

Gene: MUC19, mucin 19, oligomeric (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
MUC19 transcript	NM_173600.2:c.1661+347G>A	N/A	Intron Variant

Gene: LOC105369736, uncharacterized LOC105369736 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LOC105369736 transcript variant X4	XR_007063562.1:n.	N/A	Intron Variant
LOC105369736 transcript variant X2	XR_944866.1:n.	N/A	Intron Variant
LOC105369736 transcript variant X1	XR_944867.1:n.	N/A	Intron Variant
LOC105369736 transcript variant X5	XR_944868.3:n.	N/A	Intron Variant
LOC105369736 transcript variant X3	XR_944869.3: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 12	NC_000012.12:g.40420782=	NC_000012.12:g.40420782G>A
GRCh37.p13 chr 12	NC_000012.11:g.40814584=	NC_000012.11:g.40814584G>A
MUC19 transcript	NM_173600.2:c.1661+347=	NM_173600.2:c.1661+347G>A
MUC19 transcript	XM_003846356.2:c.1613+347=	XM_003846356.2:c.1613+347G>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#.

45 SubSNP, 19 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	WI_SSAHASNP	ss6577586	Feb 20, 2003 (111)
2	1000GENOMES	ss337295628	May 09, 2011 (134)
3	SSMP	ss658666252	Apr 25, 2013 (138)
4	EVA-GONL	ss989452987	Aug 21, 2014 (142)
5	JMKIDD_LAB	ss1078403324	Aug 21, 2014 (142)
6	1000GENOMES	ss1344704230	Aug 21, 2014 (142)
7	DDI	ss1426910617	Apr 01, 2015 (144)
8	EVA_GENOME_DK	ss1576236150	Apr 01, 2015 (144)
9	EVA_DECODE	ss1599120343	Apr 01, 2015 (144)
10	EVA_UK10K_ALSPAC	ss1628430300	Apr 01, 2015 (144)
11	EVA_UK10K_TWINSUK	ss1671424333	Apr 01, 2015 (144)
12	WEILL_CORNELL_DGM	ss1932816721	Feb 12, 2016 (147)
13	GENOMED	ss1967572097	Jul 19, 2016 (147)
14	JJLAB	ss2027159012	Sep 14, 2016 (149)
15	ILLUMINA	ss2094873685	Dec 20, 2016 (150)
16	ILLUMINA	ss2095034413	Dec 20, 2016 (150)
17	USC_VALOUEV	ss2155492125	Dec 20, 2016 (150)
18	HUMAN_LONGEVITY	ss2189144492	Dec 20, 2016 (150)
19	ILLUMINA	ss2632949984	Nov 08, 2017 (151)
20	GRF	ss2699831382	Nov 08, 2017 (151)
21	GNOMAD	ss2909608509	Nov 08, 2017 (151)
22	SWEGEN	ss3009556410	Nov 08, 2017 (151)
23	ILLUMINA	ss3651799555	Oct 12, 2018 (152)
24	EGCUT_WGS	ss3676832056	Jul 13, 2019 (153)
25	EVA_DECODE	ss3693518021	Jul 13, 2019 (153)
26	ACPOP	ss3738952232	Jul 13, 2019 (153)
27	ILLUMINA	ss3744394227	Jul 13, 2019 (153)
28	EVA	ss3750384237	Jul 13, 2019 (153)
29	KHV_HUMAN_GENOMES	ss3815713203	Jul 13, 2019 (153)
30	SGDP_PRJ	ss3878112370	Apr 27, 2020 (154)
31	KRGDB	ss3926717574	Apr 27, 2020 (154)
32	TOPMED	ss4915554068	Apr 26, 2021 (155)
33	TOMMO_GENOMICS	ss5205960195	Apr 26, 2021 (155)
34	1000G_HIGH_COVERAGE	ss5290533122	Oct 16, 2022 (156)
35	EVA	ss5405145229	Oct 16, 2022 (156)
36	HUGCELL_USP	ss5485320955	Oct 16, 2022 (156)
37	EVA	ss5510671977	Oct 16, 2022 (156)
38	1000G_HIGH_COVERAGE	ss5587885211	Oct 16, 2022 (156)
39	SANFORD_IMAGENETICS	ss5652997724	Oct 16, 2022 (156)
40	TOMMO_GENOMICS	ss5755644260	Oct 16, 2022 (156)
41	YY_MCH	ss5813228371	Oct 16, 2022 (156)
42	EVA	ss5837862780	Oct 16, 2022 (156)
43	EVA	ss5850346932	Oct 16, 2022 (156)
44	EVA	ss5904080473	Oct 16, 2022 (156)
45	EVA	ss5944355596	Oct 16, 2022 (156)
46	1000Genomes	NC_000012.11 - 40814584	Oct 12, 2018 (152)
47	1000Genomes_30x	NC_000012.12 - 40420782	Oct 16, 2022 (156)
48	The Avon Longitudinal Study of Parents and Children	NC_000012.11 - 40814584	Oct 12, 2018 (152)
49	Genetic variation in the Estonian population	NC_000012.11 - 40814584	Oct 12, 2018 (152)
50	The Danish reference pan genome	NC_000012.11 - 40814584	Apr 27, 2020 (154)
51	gnomAD - Genomes	NC_000012.12 - 40420782	Apr 26, 2021 (155)
52	Genome of the Netherlands Release 5	NC_000012.11 - 40814584	Apr 27, 2020 (154)
53	HapMap	NC_000012.12 - 40420782	Apr 27, 2020 (154)
54	KOREAN population from KRGDB	NC_000012.11 - 40814584	Apr 27, 2020 (154)
55	Northern Sweden	NC_000012.11 - 40814584	Jul 13, 2019 (153)
56	Qatari	NC_000012.11 - 40814584	Apr 27, 2020 (154)
57	SGDP_PRJ	NC_000012.11 - 40814584	Apr 27, 2020 (154)
58	Siberian	NC_000012.11 - 40814584	Apr 27, 2020 (154)
59	8.3KJPN	NC_000012.11 - 40814584	Apr 26, 2021 (155)
60	14KJPN	NC_000012.12 - 40420782	Oct 16, 2022 (156)
61	TopMed	NC_000012.12 - 40420782	Apr 26, 2021 (155)
62	UK 10K study - Twins	NC_000012.11 - 40814584	Oct 12, 2018 (152)
63	A Vietnamese Genetic Variation Database	NC_000012.11 - 40814584	Jul 13, 2019 (153)
64	ALFA	NC_000012.12 - 40420782	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
ss1599120343, ss2094873685	NC_000012.10:39100850:G:A	NC_000012.12:40420781:G:A	(self)
57441423, 31897732, 22570304, 2932461, 14235688, 33894968, 12237097, 14858651, 30129350, 8008479, 63929502, 31897732, 7079019, ss337295628, ss658666252, ss989452987, ss1078403324, ss1344704230, ss1426910617, ss1576236150, ss1628430300, ss1671424333, ss1932816721, ss1967572097, ss2027159012, ss2095034413, ss2155492125, ss2632949984, ss2699831382, ss2909608509, ss3009556410, ss3651799555, ss3676832056, ss3738952232, ss3744394227, ss3750384237, ss3878112370, ss3926717574, ss5205960195, ss5405145229, ss5510671977, ss5652997724, ss5837862780, ss5944355596	NC_000012.11:40814583:G:A	NC_000012.12:40420781:G:A	(self)
75411146, 405058568, 799249, 89481364, 131099725, 2879204189, ss2189144492, ss3693518021, ss3815713203, ss4915554068, ss5290533122, ss5485320955, ss5587885211, ss5755644260, ss5813228371, ss5850346932, ss5904080473	NC_000012.12:40420781:G:A	NC_000012.12:40420781:G:A	(self)
ss6577586	NT_029419.12:2957889:G:A	NC_000012.12:40420781: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 rs4768258

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

rs4768258