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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.

rs144411158

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr17:68555742 (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 / G>T
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.000102 (27/264690, TOPMED)
A=0.000032 (4/124754, ALFA)
A=0.000041 (5/121264, ExAC) (+ 4 more)
A=0.00014 (11/78702, PAGE_STUDY)
A=0.00015 (2/13006, GO-ESP)
A=0.0003 (2/6404, 1000G_30x)
A=0.0004 (2/5008, 1000G)
Clinical Significance
Reported in ClinVar
Gene : Consequence
FAM20A : Stop Gained
Publications
3 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 124754 G=0.999968 A=0.000032, T=0.000000
European Sub 109650 G=0.999964 A=0.000036, T=0.000000
African Sub 3774 G=1.0000 A=0.0000, T=0.0000
African Others Sub 168 G=1.000 A=0.000, T=0.000
African American Sub 3606 G=1.0000 A=0.0000, T=0.0000
Asian Sub 3274 G=1.0000 A=0.0000, T=0.0000
East Asian Sub 2648 G=1.0000 A=0.0000, T=0.0000
Other Asian Sub 626 G=1.000 A=0.000, T=0.000
Latin American 1 Sub 790 G=1.000 A=0.000, T=0.000
Latin American 2 Sub 946 G=1.000 A=0.000, T=0.000
South Asian Sub 274 G=1.000 A=0.000, T=0.000
Other Sub 6046 G=1.0000 A=0.0000, T=0.0000


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 G=0.999898 A=0.000102
Allele Frequency Aggregator Total Global 124754 G=0.999968 A=0.000032, T=0.000000
Allele Frequency Aggregator European Sub 109650 G=0.999964 A=0.000036, T=0.000000
Allele Frequency Aggregator Other Sub 6046 G=1.0000 A=0.0000, T=0.0000
Allele Frequency Aggregator African Sub 3774 G=1.0000 A=0.0000, T=0.0000
Allele Frequency Aggregator Asian Sub 3274 G=1.0000 A=0.0000, T=0.0000
Allele Frequency Aggregator Latin American 2 Sub 946 G=1.000 A=0.000, T=0.000
Allele Frequency Aggregator Latin American 1 Sub 790 G=1.000 A=0.000, T=0.000
Allele Frequency Aggregator South Asian Sub 274 G=1.000 A=0.000, T=0.000
ExAC Global Study-wide 121264 G=0.999959 A=0.000041
ExAC Europe Sub 73246 G=1.00000 A=0.00000
ExAC Asian Sub 25152 G=1.00000 A=0.00000
ExAC American Sub 11568 G=0.99991 A=0.00009
ExAC African Sub 10396 G=0.99962 A=0.00038
ExAC Other Sub 902 G=1.000 A=0.000
The PAGE Study Global Study-wide 78702 G=0.99986 A=0.00014
The PAGE Study AfricanAmerican Sub 32516 G=0.99966 A=0.00034
The PAGE Study Mexican Sub 10810 G=1.00000 A=0.00000
The PAGE Study Asian Sub 8318 G=1.0000 A=0.0000
The PAGE Study PuertoRican Sub 7918 G=1.0000 A=0.0000
The PAGE Study NativeHawaiian Sub 4534 G=1.0000 A=0.0000
The PAGE Study Cuban Sub 4230 G=1.0000 A=0.0000
The PAGE Study Dominican Sub 3828 G=1.0000 A=0.0000
The PAGE Study CentralAmerican Sub 2450 G=1.0000 A=0.0000
The PAGE Study SouthAmerican Sub 1982 G=1.0000 A=0.0000
The PAGE Study NativeAmerican Sub 1260 G=1.0000 A=0.0000
The PAGE Study SouthAsian Sub 856 G=1.000 A=0.000
GO Exome Sequencing Project Global Study-wide 13006 G=0.99985 A=0.00015
GO Exome Sequencing Project European American Sub 8600 G=1.0000 A=0.0000
GO Exome Sequencing Project African American Sub 4406 G=0.9995 A=0.0005
1000Genomes_30x Global Study-wide 6404 G=0.9997 A=0.0003
1000Genomes_30x African Sub 1786 G=0.9989 A=0.0011
1000Genomes_30x Europe Sub 1266 G=1.0000 A=0.0000
1000Genomes_30x South Asian Sub 1202 G=1.0000 A=0.0000
1000Genomes_30x East Asian Sub 1170 G=1.0000 A=0.0000
1000Genomes_30x American Sub 980 G=1.000 A=0.000
1000Genomes Global Study-wide 5008 G=0.9996 A=0.0004
1000Genomes African Sub 1322 G=0.9985 A=0.0015
1000Genomes East Asian Sub 1008 G=1.0000 A=0.0000
1000Genomes Europe Sub 1006 G=1.0000 A=0.0000
1000Genomes South Asian Sub 978 G=1.000 A=0.000
1000Genomes American Sub 694 G=1.000 A=0.000
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 17 NC_000017.11:g.68555742G>A
GRCh38.p14 chr 17 NC_000017.11:g.68555742G>T
GRCh37.p13 chr 17 NC_000017.10:g.66551883G>A
GRCh37.p13 chr 17 NC_000017.10:g.66551883G>T
FAM20A RefSeqGene NG_029809.1:g.50213C>T
FAM20A RefSeqGene NG_029809.1:g.50213C>A
Gene: FAM20A, FAM20A golgi associated secretory pathway pseudokinase (minus strand)
Molecule type Change Amino acid[Codon] SO Term
FAM20A transcript variant 3 NM_001243746.2:c.-9= N/A 5 Prime UTR Variant
FAM20A transcript variant 1 NM_017565.4:c.406C>T R [CGA] > * [TGA] Coding Sequence Variant
pseudokinase FAM20A isoform a precursor NP_060035.2:p.Arg136Ter R (Arg) > * (Ter) Stop Gained
FAM20A transcript variant 1 NM_017565.4:c.406C>A R [CGA] > R [AGA] Coding Sequence Variant
pseudokinase FAM20A isoform a precursor NP_060035.2:p.Arg136= R (Arg) > R (Arg) Synonymous Variant
FAM20A transcript variant 2 NR_027751.2:n.100C>T N/A Non Coding Transcript Variant
FAM20A transcript variant 2 NR_027751.2:n.100C>A N/A Non Coding Transcript Variant
FAM20A transcript variant X3 XM_006721959.4:c.-9= N/A 5 Prime UTR Variant
FAM20A transcript variant X4 XM_017024781.3:c.406C>T R [CGA] > * [TGA] Coding Sequence Variant
pseudokinase FAM20A isoform X2 XP_016880270.1:p.Arg136Ter R (Arg) > * (Ter) Stop Gained
FAM20A transcript variant X4 XM_017024781.3:c.406C>A R [CGA] > R [AGA] Coding Sequence Variant
pseudokinase FAM20A isoform X2 XP_016880270.1:p.Arg136= R (Arg) > R (Arg) Synonymous Variant
FAM20A transcript variant X6 XM_047436319.1:c.406C>T R [CGA] > * [TGA] Coding Sequence Variant
pseudokinase FAM20A isoform X3 XP_047292275.1:p.Arg136Ter R (Arg) > * (Ter) Stop Gained
FAM20A transcript variant X6 XM_047436319.1:c.406C>A R [CGA] > R [AGA] Coding Sequence Variant
pseudokinase FAM20A isoform X3 XP_047292275.1:p.Arg136= R (Arg) > R (Arg) Synonymous Variant
FAM20A transcript variant X7 XM_011524918.4:c.406C>T R [CGA] > * [TGA] Coding Sequence Variant
pseudokinase FAM20A isoform X4 XP_011523220.1:p.Arg136Ter R (Arg) > * (Ter) Stop Gained
FAM20A transcript variant X7 XM_011524918.4:c.406C>A R [CGA] > R [AGA] Coding Sequence Variant
pseudokinase FAM20A isoform X4 XP_011523220.1:p.Arg136= R (Arg) > R (Arg) Synonymous Variant
FAM20A transcript variant X1 XR_002958041.2:n.1107C>T N/A Non Coding Transcript Variant
FAM20A transcript variant X1 XR_002958041.2:n.1107C>A N/A Non Coding Transcript Variant
FAM20A transcript variant X2 XR_934487.4:n.1107C>T N/A Non Coding Transcript Variant
FAM20A transcript variant X2 XR_934487.4:n.1107C>A N/A Non Coding Transcript Variant
FAM20A transcript variant X5 XR_001752543.3:n.1107C>T N/A Non Coding Transcript Variant
FAM20A transcript variant X5 XR_001752543.3:n.1107C>A N/A Non Coding Transcript Variant
FAM20A transcript variant X8 XR_429905.3:n.1107C>T N/A Non Coding Transcript Variant
FAM20A transcript variant X8 XR_429905.3:n.1107C>A N/A Non Coding 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.

Allele: A (allele ID: 39836 )
ClinVar Accession Disease Names Clinical Significance
RCV000023864.7 Amelogenesis imperfecta type 1G Pathogenic
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 G= A T
GRCh38.p14 chr 17 NC_000017.11:g.68555742= NC_000017.11:g.68555742G>A NC_000017.11:g.68555742G>T
GRCh37.p13 chr 17 NC_000017.10:g.66551883= NC_000017.10:g.66551883G>A NC_000017.10:g.66551883G>T
FAM20A RefSeqGene NG_029809.1:g.50213= NG_029809.1:g.50213C>T NG_029809.1:g.50213C>A
FAM20A transcript variant 1 NM_017565.4:c.406= NM_017565.4:c.406C>T NM_017565.4:c.406C>A
FAM20A transcript variant 1 NM_017565.3:c.406= NM_017565.3:c.406C>T NM_017565.3:c.406C>A
FAM20A transcript variant 3 NM_001243746.2:c.-9= NM_001243746.2:c.-9C>T NM_001243746.2:c.-9C>A
FAM20A transcript variant 3 NM_001243746.1:c.-9= NM_001243746.1:c.-9C>T NM_001243746.1:c.-9C>A
FAM20A transcript variant 2 NR_027751.2:n.100= NR_027751.2:n.100C>T NR_027751.2:n.100C>A
FAM20A transcript variant 2 NR_027751.1:n.100= NR_027751.1:n.100C>T NR_027751.1:n.100C>A
FAM20A transcript variant X3 XM_006721959.4:c.-9= XM_006721959.4:c.-9C>T XM_006721959.4:c.-9C>A
FAM20A transcript variant X3 XM_006721959.3:c.-9= XM_006721959.3:c.-9C>T XM_006721959.3:c.-9C>A
FAM20A transcript variant X3 XM_006721959.2:c.-9= XM_006721959.2:c.-9C>T XM_006721959.2:c.-9C>A
FAM20A transcript variant X2 XM_006721959.1:c.-9= XM_006721959.1:c.-9C>T XM_006721959.1:c.-9C>A
FAM20A transcript variant X2 XR_934487.4:n.1107= XR_934487.4:n.1107C>T XR_934487.4:n.1107C>A
FAM20A transcript variant X2 XR_934487.3:n.477= XR_934487.3:n.477C>T XR_934487.3:n.477C>A
FAM20A transcript variant X2 XR_934487.2:n.534= XR_934487.2:n.534C>T XR_934487.2:n.534C>A
FAM20A transcript variant X3 XR_934487.1:n.534= XR_934487.1:n.534C>T XR_934487.1:n.534C>A
FAM20A transcript variant X7 XM_011524918.4:c.406= XM_011524918.4:c.406C>T XM_011524918.4:c.406C>A
FAM20A transcript variant X7 XM_011524918.3:c.406= XM_011524918.3:c.406C>T XM_011524918.3:c.406C>A
FAM20A transcript variant X7 XM_011524918.2:c.406= XM_011524918.2:c.406C>T XM_011524918.2:c.406C>A
FAM20A transcript variant X6 XM_011524918.1:c.406= XM_011524918.1:c.406C>T XM_011524918.1:c.406C>A
FAM20A transcript variant X4 XM_017024781.3:c.406= XM_017024781.3:c.406C>T XM_017024781.3:c.406C>A
FAM20A transcript variant X4 XM_017024781.2:c.406= XM_017024781.2:c.406C>T XM_017024781.2:c.406C>A
FAM20A transcript variant X4 XM_017024781.1:c.406= XM_017024781.1:c.406C>T XM_017024781.1:c.406C>A
FAM20A transcript variant X5 XR_001752543.3:n.1107= XR_001752543.3:n.1107C>T XR_001752543.3:n.1107C>A
FAM20A transcript variant X5 XR_001752543.2:n.477= XR_001752543.2:n.477C>T XR_001752543.2:n.477C>A
FAM20A transcript variant X5 XR_001752543.1:n.534= XR_001752543.1:n.534C>T XR_001752543.1:n.534C>A
FAM20A transcript variant X8 XR_429905.3:n.1107= XR_429905.3:n.1107C>T XR_429905.3:n.1107C>A
FAM20A transcript variant X8 XR_429905.2:n.477= XR_429905.2:n.477C>T XR_429905.2:n.477C>A
FAM20A transcript variant X8 XR_429905.1:n.534= XR_429905.1:n.534C>T XR_429905.1:n.534C>A
FAM20A transcript variant X1 XR_002958041.2:n.1107= XR_002958041.2:n.1107C>T XR_002958041.2:n.1107C>A
FAM20A transcript variant X1 XR_002958041.1:n.477= XR_002958041.1:n.477C>T XR_002958041.1:n.477C>A
FAM20A transcript variant X6 XM_047436319.1:c.406= XM_047436319.1:c.406C>T XM_047436319.1:c.406C>A
pseudokinase FAM20A isoform a precursor NP_060035.2:p.Arg136= NP_060035.2:p.Arg136Ter NP_060035.2:p.Arg136=
pseudokinase FAM20A isoform X4 XP_011523220.1:p.Arg136= XP_011523220.1:p.Arg136Ter XP_011523220.1:p.Arg136=
pseudokinase FAM20A isoform X2 XP_016880270.1:p.Arg136= XP_016880270.1:p.Arg136Ter XP_016880270.1:p.Arg136=
pseudokinase FAM20A isoform X3 XP_047292275.1:p.Arg136= XP_047292275.1:p.Arg136Ter XP_047292275.1:p.Arg136=
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#.

30 SubSNP, 11 Frequency, 1 ClinVar submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss339814913 May 09, 2011 (134)
2 1000GENOMES ss491130384 May 04, 2012 (137)
3 WARNICH_LAB ss678423127 Apr 25, 2013 (138)
4 NHLBI-ESP ss713415339 Apr 25, 2013 (138)
5 OMIM-CURATED-RECORDS ss825077688 Jun 20, 2013 (137)
6 1000GENOMES ss1359347326 Aug 21, 2014 (142)
7 EVA_EXAC ss1692933148 Apr 01, 2015 (144)
8 ILLUMINA ss1946466196 Feb 12, 2016 (147)
9 ILLUMINA ss1959763745 Feb 12, 2016 (147)
10 HUMAN_LONGEVITY ss2218217664 Dec 20, 2016 (150)
11 GNOMAD ss2742958053 Nov 08, 2017 (151)
12 GNOMAD ss2749847214 Nov 08, 2017 (151)
13 GNOMAD ss2951916930 Nov 08, 2017 (151)
14 AFFY ss2985103077 Nov 08, 2017 (151)
15 ILLUMINA ss3625717348 Oct 12, 2018 (152)
16 ILLUMINA ss3644693844 Oct 12, 2018 (152)
17 ILLUMINA ss3653874896 Oct 12, 2018 (152)
18 ILLUMINA ss3744152440 Jul 13, 2019 (153)
19 PAGE_CC ss3771940801 Jul 13, 2019 (153)
20 EVA ss3825145411 Apr 27, 2020 (154)
21 TOPMED ss5042175487 Apr 27, 2021 (155)
22 1000G_HIGH_COVERAGE ss5303759123 Oct 16, 2022 (156)
23 EVA ss5428710634 Oct 16, 2022 (156)
24 HUGCELL_USP ss5496739482 Oct 16, 2022 (156)
25 1000G_HIGH_COVERAGE ss5607780408 Oct 16, 2022 (156)
26 SANFORD_IMAGENETICS ss5660445147 Oct 16, 2022 (156)
27 EVA ss5847804996 Oct 16, 2022 (156)
28 EVA ss5914628504 Oct 16, 2022 (156)
29 EVA ss5951842195 Oct 16, 2022 (156)
30 EVA ss5979512919 Oct 16, 2022 (156)
31 1000Genomes NC_000017.10 - 66551883 Oct 12, 2018 (152)
32 1000Genomes_30x NC_000017.11 - 68555742 Oct 16, 2022 (156)
33 ExAC NC_000017.10 - 66551883 Oct 12, 2018 (152)
34 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 512472103 (NC_000017.11:68555741:G:A 12/140188)
Row 512472104 (NC_000017.11:68555741:G:T 0/140188)

- Apr 27, 2021 (155)
35 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 512472103 (NC_000017.11:68555741:G:A 12/140188)
Row 512472104 (NC_000017.11:68555741:G:T 0/140188)

- Apr 27, 2021 (155)
36 gnomAD - Exomes

Submission ignored due to conflicting rows:
Row 12265432 (NC_000017.10:66551882:G:G 251287/251298, NC_000017.10:66551882:G:A 11/251298)
Row 12265433 (NC_000017.10:66551882:G:G 251297/251298, NC_000017.10:66551882:G:T 1/251298)

- Jul 13, 2019 (153)
37 gnomAD - Exomes

Submission ignored due to conflicting rows:
Row 12265432 (NC_000017.10:66551882:G:G 251287/251298, NC_000017.10:66551882:G:A 11/251298)
Row 12265433 (NC_000017.10:66551882:G:G 251297/251298, NC_000017.10:66551882:G:T 1/251298)

- Jul 13, 2019 (153)
38 GO Exome Sequencing Project NC_000017.10 - 66551883 Oct 12, 2018 (152)
39 The PAGE Study NC_000017.11 - 68555742 Jul 13, 2019 (153)
40 TopMed NC_000017.11 - 68555742 Apr 27, 2021 (155)
41 ALFA NC_000017.11 - 68555742 Apr 27, 2021 (155)
42 ClinVar RCV000023864.7 Oct 16, 2022 (156)
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
72615978, 3388319, 1602472, ss339814913, ss491130384, ss678423127, ss713415339, ss1359347326, ss1692933148, ss1946466196, ss1959763745, ss2742958053, ss2749847214, ss2951916930, ss2985103077, ss3625717348, ss3644693844, ss3653874896, ss3744152440, ss3825145411, ss5428710634, ss5660445147, ss5847804996, ss5951842195, ss5979512919 NC_000017.10:66551882:G:A NC_000017.11:68555741:G:A (self)
RCV000023864.7, 95306343, 1162270, 257721149, 13313061556, ss825077688, ss2218217664, ss3771940801, ss5042175487, ss5303759123, ss5496739482, ss5607780408, ss5914628504 NC_000017.11:68555741:G:A NC_000017.11:68555741:G:A (self)
ss2742958053 NC_000017.10:66551882:G:T NC_000017.11:68555741:G:T (self)
13313061556 NC_000017.11:68555741:G:T NC_000017.11:68555741:G:T (self)
Help

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

3 citations for rs144411158
PMID Title Author Year Journal
18597613 Case reports of a new syndrome associating gingival fibromatosis and dental abnormalities in a consanguineous family. Martelli-Júnior H et al. 2008 Journal of periodontology
21549343 Whole-Exome sequencing identifies FAM20A mutations as a cause of amelogenesis imperfecta and gingival hyperplasia syndrome. O'Sullivan J et al. 2011 American journal of human genetics
23434854 Nephrocalcinosis (enamel renal syndrome) caused by autosomal recessive FAM20A mutations. Jaureguiberry G et al. 2012 Nephron. Physiology
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