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dbSNP Short Genetic Variations

Examples: rs268, BRCA1 and more Advanced search

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.

rs149401300

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr19:32482227 (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=0.000695 (184/264690, TOPMED)
T=0.000394 (98/248844, GnomAD_exome)
T=0.000487 (96/197114, ALFA) (+ 4 more)
T=0.000535 (75/140150, GnomAD)
T=0.000470 (57/121216, ExAC)
T=0.00011 (9/78698, PAGE_STUDY)
T=0.00008 (1/13006, GO-ESP)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
DPY19L3 : Missense 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 213524 C=0.999541 T=0.000459
European Sub 178026 C=0.999517 T=0.000483
African Sub 9710 C=1.0000 T=0.0000
African Others Sub 354 C=1.000 T=0.000
African American Sub 9356 C=1.0000 T=0.0000
Asian Sub 6346 C=1.0000 T=0.0000
East Asian Sub 4500 C=1.0000 T=0.0000
Other Asian Sub 1846 C=1.0000 T=0.0000
Latin American 1 Sub 796 C=0.999 T=0.001
Latin American 2 Sub 968 C=0.998 T=0.002
South Asian Sub 276 C=1.000 T=0.000
Other Sub 17402 C=0.99948 T=0.00052


Help

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
TopMed Global Study-wide 264690 C=0.999305 T=0.000695
gnomAD - Exomes Global Study-wide 248844 C=0.999606 T=0.000394
gnomAD - Exomes European Sub 134386 C=0.999434 T=0.000566
gnomAD - Exomes Asian Sub 48236 C=0.99985 T=0.00015
gnomAD - Exomes American Sub 33938 C=0.99971 T=0.00029
gnomAD - Exomes African Sub 16228 C=1.00000 T=0.00000
gnomAD - Exomes Ashkenazi Jewish Sub 9980 C=0.9999 T=0.0001
gnomAD - Exomes Other Sub 6076 C=0.9993 T=0.0007
Allele Frequency Aggregator Total Global 197114 C=0.999513 T=0.000487
Allele Frequency Aggregator European Sub 167888 C=0.999500 T=0.000500
Allele Frequency Aggregator Other Sub 15968 C=0.99944 T=0.00056
Allele Frequency Aggregator Asian Sub 6346 C=1.0000 T=0.0000
Allele Frequency Aggregator African Sub 4872 C=1.0000 T=0.0000
Allele Frequency Aggregator Latin American 2 Sub 968 C=0.998 T=0.002
Allele Frequency Aggregator Latin American 1 Sub 796 C=0.999 T=0.001
Allele Frequency Aggregator South Asian Sub 276 C=1.000 T=0.000
gnomAD - Genomes Global Study-wide 140150 C=0.999465 T=0.000535
gnomAD - Genomes European Sub 75896 C=0.99904 T=0.00096
gnomAD - Genomes African Sub 42004 C=1.00000 T=0.00000
gnomAD - Genomes American Sub 13656 C=0.99985 T=0.00015
gnomAD - Genomes Ashkenazi Jewish Sub 3320 C=1.0000 T=0.0000
gnomAD - Genomes East Asian Sub 3128 C=1.0000 T=0.0000
gnomAD - Genomes Other Sub 2146 C=1.0000 T=0.0000
ExAC Global Study-wide 121216 C=0.999530 T=0.000470
ExAC Europe Sub 73268 C=0.99929 T=0.00071
ExAC Asian Sub 25068 C=0.99988 T=0.00012
ExAC American Sub 11574 C=0.99991 T=0.00009
ExAC African Sub 10398 C=1.00000 T=0.00000
ExAC Other Sub 908 C=0.999 T=0.001
The PAGE Study Global Study-wide 78698 C=0.99989 T=0.00011
The PAGE Study AfricanAmerican Sub 32514 C=1.00000 T=0.00000
The PAGE Study Mexican Sub 10808 C=0.99972 T=0.00028
The PAGE Study Asian Sub 8318 C=1.0000 T=0.0000
The PAGE Study PuertoRican Sub 7918 C=1.0000 T=0.0000
The PAGE Study NativeHawaiian Sub 4534 C=1.0000 T=0.0000
The PAGE Study Cuban Sub 4230 C=0.9995 T=0.0005
The PAGE Study Dominican Sub 3828 C=0.9995 T=0.0005
The PAGE Study CentralAmerican Sub 2450 C=0.9996 T=0.0004
The PAGE Study SouthAmerican Sub 1982 C=0.9995 T=0.0005
The PAGE Study NativeAmerican Sub 1260 C=1.0000 T=0.0000
The PAGE Study SouthAsian Sub 856 C=1.000 T=0.000
GO Exome Sequencing Project Global Study-wide 13006 C=0.99992 T=0.00008
GO Exome Sequencing Project European American Sub 8600 C=0.9999 T=0.0001
GO Exome Sequencing Project African American Sub 4406 C=1.0000 T=0.0000
Help

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 19 NC_000019.10:g.32482227C>T
GRCh37.p13 chr 19 NC_000019.9:g.32973133C>T
Gene: DPY19L3, dpy-19 like C-mannosyltransferase 3 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
DPY19L3 transcript variant 2 NM_001172774.2:c.2138C>T S [TCC] > F [TTC] Coding Sequence Variant
protein C-mannosyl-transferase DPY19L3 NP_001166245.1:p.Ser713Phe S (Ser) > F (Phe) Missense Variant
DPY19L3 transcript variant 1 NM_207325.3:c.2138C>T S [TCC] > F [TTC] Coding Sequence Variant
protein C-mannosyl-transferase DPY19L3 NP_997208.2:p.Ser713Phe S (Ser) > F (Phe) Missense Variant
DPY19L3 transcript variant X6 XM_047438249.1:c. N/A Genic Downstream Transcript Variant
DPY19L3 transcript variant X7 XM_047438250.1:c. N/A Genic Downstream Transcript Variant
DPY19L3 transcript variant X8 XM_047438251.1:c. N/A Genic Downstream Transcript Variant
DPY19L3 transcript variant X10 XM_047438252.1:c. N/A Genic Downstream Transcript Variant
DPY19L3 transcript variant X12 XM_047438253.1:c. N/A Genic Downstream Transcript Variant
DPY19L3 transcript variant X3 XM_017026366.1:c.2036C>T S [TCC] > F [TTC] Coding Sequence Variant
probable C-mannosyltransferase DPY19L3 isoform X2 XP_016881855.1:p.Ser679Phe S (Ser) > F (Phe) Missense Variant
DPY19L3 transcript variant X1 XM_011526526.3:c.2138C>T S [TCC] > F [TTC] Coding Sequence Variant
probable C-mannosyltransferase DPY19L3 isoform X1 XP_011524828.1:p.Ser713Phe S (Ser) > F (Phe) Missense Variant
DPY19L3 transcript variant X2 XM_047438247.1:c.2036C>T S [TCC] > F [TTC] Coding Sequence Variant
probable C-mannosyltransferase DPY19L3 isoform X2 XP_047294203.1:p.Ser679Phe S (Ser) > F (Phe) Missense Variant
DPY19L3 transcript variant X4 XM_047438248.1:c.2036C>T S [TCC] > F [TTC] Coding Sequence Variant
probable C-mannosyltransferase DPY19L3 isoform X2 XP_047294204.1:p.Ser679Phe S (Ser) > F (Phe) Missense Variant
DPY19L3 transcript variant X11 XM_006723045.2:c.1550C>T S [TCC] > F [TTC] Coding Sequence Variant
probable C-mannosyltransferase DPY19L3 isoform X5 XP_006723108.1:p.Ser517Phe S (Ser) > F (Phe) Missense Variant
DPY19L3 transcript variant X13 XM_017026367.3:c.1349C>T S [TCC] > F [TTC] Coding Sequence Variant
probable C-mannosyltransferase DPY19L3 isoform X7 XP_016881856.1:p.Ser450Phe S (Ser) > F (Phe) Missense Variant
DPY19L3 transcript variant X5 XR_007066627.1:n. N/A Genic Downstream Transcript Variant
DPY19L3 transcript variant X9 XR_007066628.1:n. N/A Genic Downstream Transcript Variant
Help

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
Help

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 19 NC_000019.10:g.32482227= NC_000019.10:g.32482227C>T
GRCh37.p13 chr 19 NC_000019.9:g.32973133= NC_000019.9:g.32973133C>T
DPY19L3 transcript variant 1 NM_207325.3:c.2138= NM_207325.3:c.2138C>T
DPY19L3 transcript variant 1 NM_207325.2:c.2138= NM_207325.2:c.2138C>T
DPY19L3 transcript variant X1 XM_011526526.3:c.2138= XM_011526526.3:c.2138C>T
DPY19L3 transcript variant X2 XM_011526526.2:c.2138= XM_011526526.2:c.2138C>T
DPY19L3 transcript variant X1 XM_011526526.1:c.2138= XM_011526526.1:c.2138C>T
DPY19L3 transcript variant X13 XM_017026367.3:c.1349= XM_017026367.3:c.1349C>T
DPY19L3 transcript variant X9 XM_017026367.2:c.1349= XM_017026367.2:c.1349C>T
DPY19L3 transcript variant X9 XM_017026367.1:c.1349= XM_017026367.1:c.1349C>T
DPY19L3 transcript variant 2 NM_001172774.2:c.2138= NM_001172774.2:c.2138C>T
DPY19L3 transcript variant 2 NM_001172774.1:c.2138= NM_001172774.1:c.2138C>T
DPY19L3 transcript variant X11 XM_006723045.2:c.1550= XM_006723045.2:c.1550C>T
DPY19L3 transcript variant X8 XM_006723045.1:c.1550= XM_006723045.1:c.1550C>T
DPY19L3 transcript variant X3 XM_017026366.1:c.2036= XM_017026366.1:c.2036C>T
DPY19L3 transcript variant X4 XM_047438248.1:c.2036= XM_047438248.1:c.2036C>T
DPY19L3 transcript variant X2 XM_047438247.1:c.2036= XM_047438247.1:c.2036C>T
protein C-mannosyl-transferase DPY19L3 NP_997208.2:p.Ser713= NP_997208.2:p.Ser713Phe
probable C-mannosyltransferase DPY19L3 isoform X1 XP_011524828.1:p.Ser713= XP_011524828.1:p.Ser713Phe
probable C-mannosyltransferase DPY19L3 isoform X7 XP_016881856.1:p.Ser450= XP_016881856.1:p.Ser450Phe
protein C-mannosyl-transferase DPY19L3 NP_001166245.1:p.Ser713= NP_001166245.1:p.Ser713Phe
probable C-mannosyltransferase DPY19L3 isoform X5 XP_006723108.1:p.Ser517= XP_006723108.1:p.Ser517Phe
probable C-mannosyltransferase DPY19L3 isoform X2 XP_016881855.1:p.Ser679= XP_016881855.1:p.Ser679Phe
probable C-mannosyltransferase DPY19L3 isoform X2 XP_047294204.1:p.Ser679= XP_047294204.1:p.Ser679Phe
probable C-mannosyltransferase DPY19L3 isoform X2 XP_047294203.1:p.Ser679= XP_047294203.1:p.Ser679Phe
Help

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#.

34 SubSNP, 7 Frequency submissions
No Submitter Submission ID Date (Build)
1 NHLBI-ESP ss342493175 May 09, 2011 (134)
2 EXOME_CHIP ss491544635 May 04, 2012 (137)
3 ILLUMINA ss780744088 Sep 08, 2015 (146)
4 ILLUMINA ss783421633 Sep 08, 2015 (146)
5 EVA_EXAC ss1693519346 Apr 01, 2015 (144)
6 ILLUMINA ss1752281124 Sep 08, 2015 (146)
7 ILLUMINA ss1917935712 Feb 12, 2016 (147)
8 ILLUMINA ss1946532898 Feb 12, 2016 (147)
9 ILLUMINA ss1959856464 Feb 12, 2016 (147)
10 HUMAN_LONGEVITY ss2225355632 Dec 20, 2016 (150)
11 GNOMAD ss2743865005 Nov 08, 2017 (151)
12 GNOMAD ss2750146827 Nov 08, 2017 (151)
13 GNOMAD ss2962256004 Nov 08, 2017 (151)
14 AFFY ss2985138412 Nov 08, 2017 (151)
15 ILLUMINA ss3021898047 Nov 08, 2017 (151)
16 ILLUMINA ss3627919800 Oct 12, 2018 (152)
17 ILLUMINA ss3634731779 Oct 12, 2018 (152)
18 ILLUMINA ss3640439087 Oct 12, 2018 (152)
19 ILLUMINA ss3644721442 Oct 12, 2018 (152)
20 ILLUMINA ss3652323725 Oct 12, 2018 (152)
21 ILLUMINA ss3653910800 Oct 12, 2018 (152)
22 EVA_DECODE ss3702659816 Jul 13, 2019 (153)
23 ILLUMINA ss3725722456 Jul 13, 2019 (153)
24 ILLUMINA ss3744462825 Jul 13, 2019 (153)
25 ILLUMINA ss3745031803 Jul 13, 2019 (153)
26 PAGE_CC ss3772008307 Jul 13, 2019 (153)
27 ILLUMINA ss3772528978 Jul 13, 2019 (153)
28 EVA ss3825270852 Apr 27, 2020 (154)
29 TOPMED ss5073054765 Apr 26, 2021 (155)
30 HUGCELL_USP ss5499605204 Oct 16, 2022 (156)
31 EVA ss5624088741 Oct 16, 2022 (156)
32 EVA ss5840476143 Oct 16, 2022 (156)
33 EVA ss5847841316 Oct 16, 2022 (156)
34 EVA ss5953702525 Oct 16, 2022 (156)
35 ExAC NC_000019.9 - 32973133 Oct 12, 2018 (152)
36 gnomAD - Genomes NC_000019.10 - 32482227 Apr 26, 2021 (155)
37 gnomAD - Exomes NC_000019.9 - 32973133 Jul 13, 2019 (153)
38 GO Exome Sequencing Project NC_000019.9 - 32973133 Oct 12, 2018 (152)
39 The PAGE Study NC_000019.10 - 32482227 Jul 13, 2019 (153)
40 TopMed NC_000019.10 - 32482227 Apr 26, 2021 (155)
41 ALFA NC_000019.10 - 32482227 Apr 26, 2021 (155)
Help

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
4017910, 13178430, 1727826, ss342493175, ss491544635, ss780744088, ss783421633, ss1693519346, ss1752281124, ss1917935712, ss1946532898, ss1959856464, ss2743865005, ss2750146827, ss2962256004, ss2985138412, ss3021898047, ss3627919800, ss3634731779, ss3640439087, ss3644721442, ss3652323725, ss3653910800, ss3744462825, ss3745031803, ss3772528978, ss3825270852, ss5624088741, ss5840476143, ss5847841316, ss5953702525 NC_000019.9:32973132:C:T NC_000019.10:32482226:C:T (self)
538521645, 1229776, 288600429, 1365317292, ss2225355632, ss3702659816, ss3725722456, ss3772008307, ss5073054765, ss5499605204 NC_000019.10:32482226:C:T NC_000019.10:32482226:C:T (self)
Help

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

No publications for rs149401300

Help

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.

Software version is: 2.0.1.post761+d5e8e07