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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.

rs1486542868

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr1:234459262 (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>C
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.000008 (2/249986, GnomAD_exome)
C=0.000007 (1/140216, GnomAD)
A=0.00000 (0/10680, ALFA) (+ 1 more)
C=0.00000 (0/10680, ALFA)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
TARBP1 : 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: 20231103111315
Population Group Sample Size Ref Allele Alt Allele Ref HMOZ Alt HMOZ HTRZ HWEP
Total Global 10680 G=1.00000 A=0.00000, C=0.00000 1.0 0.0 0.0 N/A
European Sub 6962 G=1.0000 A=0.0000, C=0.0000 1.0 0.0 0.0 N/A
African Sub 2294 G=1.0000 A=0.0000, C=0.0000 1.0 0.0 0.0 N/A
African Others Sub 84 G=1.00 A=0.00, C=0.00 1.0 0.0 0.0 N/A
African American Sub 2210 G=1.0000 A=0.0000, C=0.0000 1.0 0.0 0.0 N/A
Asian Sub 108 G=1.000 A=0.000, C=0.000 1.0 0.0 0.0 N/A
East Asian Sub 84 G=1.00 A=0.00, C=0.00 1.0 0.0 0.0 N/A
Other Asian Sub 24 G=1.00 A=0.00, C=0.00 1.0 0.0 0.0 N/A
Latin American 1 Sub 146 G=1.000 A=0.000, C=0.000 1.0 0.0 0.0 N/A
Latin American 2 Sub 610 G=1.000 A=0.000, C=0.000 1.0 0.0 0.0 N/A
South Asian Sub 94 G=1.00 A=0.00, C=0.00 1.0 0.0 0.0 N/A
Other Sub 466 G=1.000 A=0.000, C=0.000 1.0 0.0 0.0 N/A


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
gnomAD - Exomes Global Study-wide 249986 G=0.999992 A=0.000008
gnomAD - Exomes European Sub 134848 G=1.000000 A=0.000000
gnomAD - Exomes Asian Sub 48608 G=1.00000 A=0.00000
gnomAD - Exomes American Sub 34160 G=0.99994 A=0.00006
gnomAD - Exomes African Sub 16228 G=1.00000 A=0.00000
gnomAD - Exomes Ashkenazi Jewish Sub 10038 G=1.00000 A=0.00000
gnomAD - Exomes Other Sub 6104 G=1.0000 A=0.0000
gnomAD - Genomes Global Study-wide 140216 G=0.999993 C=0.000007
gnomAD - Genomes European Sub 75944 G=0.99999 C=0.00001
gnomAD - Genomes African Sub 42016 G=1.00000 C=0.00000
gnomAD - Genomes American Sub 13654 G=1.00000 C=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3324 G=1.0000 C=0.0000
gnomAD - Genomes East Asian Sub 3130 G=1.0000 C=0.0000
gnomAD - Genomes Other Sub 2148 G=1.0000 C=0.0000
Allele Frequency Aggregator Total Global 10680 G=1.00000 A=0.00000, C=0.00000
Allele Frequency Aggregator European Sub 6962 G=1.0000 A=0.0000, C=0.0000
Allele Frequency Aggregator African Sub 2294 G=1.0000 A=0.0000, C=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 G=1.000 A=0.000, C=0.000
Allele Frequency Aggregator Other Sub 466 G=1.000 A=0.000, C=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 G=1.000 A=0.000, C=0.000
Allele Frequency Aggregator Asian Sub 108 G=1.000 A=0.000, C=0.000
Allele Frequency Aggregator South Asian Sub 94 G=1.00 A=0.00, C=0.00
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 1 NC_000001.11:g.234459262G>A
GRCh38.p14 chr 1 NC_000001.11:g.234459262G>C
GRCh37.p13 chr 1 NC_000001.10:g.234595008G>A
GRCh37.p13 chr 1 NC_000001.10:g.234595008G>C
Gene: TARBP1, TAR (HIV-1) RNA binding protein 1 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
TARBP1 transcript NM_005646.4:c.1600C>T L [CTT] > F [TTT] Coding Sequence Variant
probable methyltransferase TARBP1 NP_005637.3:p.Leu534Phe L (Leu) > F (Phe) Missense Variant
TARBP1 transcript NM_005646.4:c.1600C>G L [CTT] > V [GTT] Coding Sequence Variant
probable methyltransferase TARBP1 NP_005637.3:p.Leu534Val L (Leu) > V (Val) Missense Variant
TARBP1 transcript variant X14 XM_017002196.2:c. N/A Genic Upstream Transcript Variant
TARBP1 transcript variant X16 XM_047429097.1:c. N/A Genic Upstream Transcript Variant
TARBP1 transcript variant X1 XM_005273234.4:c.1600C>T L [CTT] > F [TTT] Coding Sequence Variant
probable methyltransferase TARBP1 isoform X1 XP_005273291.1:p.Leu534Phe L (Leu) > F (Phe) Missense Variant
TARBP1 transcript variant X1 XM_005273234.4:c.1600C>G L [CTT] > V [GTT] Coding Sequence Variant
probable methyltransferase TARBP1 isoform X1 XP_005273291.1:p.Leu534Val L (Leu) > V (Val) Missense Variant
TARBP1 transcript variant X2 XM_011544263.3:c.1600C>T L [CTT] > F [TTT] Coding Sequence Variant
probable methyltransferase TARBP1 isoform X2 XP_011542565.1:p.Leu534Phe L (Leu) > F (Phe) Missense Variant
TARBP1 transcript variant X2 XM_011544263.3:c.1600C>G L [CTT] > V [GTT] Coding Sequence Variant
probable methyltransferase TARBP1 isoform X2 XP_011542565.1:p.Leu534Val L (Leu) > V (Val) Missense Variant
TARBP1 transcript variant X3 XM_047429060.1:c.1600C>T L [CTT] > F [TTT] Coding Sequence Variant
probable methyltransferase TARBP1 isoform X3 XP_047285016.1:p.Leu534Phe L (Leu) > F (Phe) Missense Variant
TARBP1 transcript variant X3 XM_047429060.1:c.1600C>G L [CTT] > V [GTT] Coding Sequence Variant
probable methyltransferase TARBP1 isoform X3 XP_047285016.1:p.Leu534Val L (Leu) > V (Val) Missense Variant
TARBP1 transcript variant X4 XM_047429061.1:c.1600C>T L [CTT] > F [TTT] Coding Sequence Variant
probable methyltransferase TARBP1 isoform X4 XP_047285017.1:p.Leu534Phe L (Leu) > F (Phe) Missense Variant
TARBP1 transcript variant X4 XM_047429061.1:c.1600C>G L [CTT] > V [GTT] Coding Sequence Variant
probable methyltransferase TARBP1 isoform X4 XP_047285017.1:p.Leu534Val L (Leu) > V (Val) Missense Variant
TARBP1 transcript variant X7 XM_047429067.1:c.1600C>T L [CTT] > F [TTT] Coding Sequence Variant
probable methyltransferase TARBP1 isoform X5 XP_047285023.1:p.Leu534Phe L (Leu) > F (Phe) Missense Variant
TARBP1 transcript variant X7 XM_047429067.1:c.1600C>G L [CTT] > V [GTT] Coding Sequence Variant
probable methyltransferase TARBP1 isoform X5 XP_047285023.1:p.Leu534Val L (Leu) > V (Val) Missense Variant
TARBP1 transcript variant X8 XM_047429068.1:c.1600C>T L [CTT] > F [TTT] Coding Sequence Variant
probable methyltransferase TARBP1 isoform X6 XP_047285024.1:p.Leu534Phe L (Leu) > F (Phe) Missense Variant
TARBP1 transcript variant X8 XM_047429068.1:c.1600C>G L [CTT] > V [GTT] Coding Sequence Variant
probable methyltransferase TARBP1 isoform X6 XP_047285024.1:p.Leu534Val L (Leu) > V (Val) Missense Variant
TARBP1 transcript variant X9 XM_047429072.1:c.1600C>T L [CTT] > F [TTT] Coding Sequence Variant
probable methyltransferase TARBP1 isoform X7 XP_047285028.1:p.Leu534Phe L (Leu) > F (Phe) Missense Variant
TARBP1 transcript variant X9 XM_047429072.1:c.1600C>G L [CTT] > V [GTT] Coding Sequence Variant
probable methyltransferase TARBP1 isoform X7 XP_047285028.1:p.Leu534Val L (Leu) > V (Val) Missense Variant
TARBP1 transcript variant X10 XM_047429073.1:c.1600C>T L [CTT] > F [TTT] Coding Sequence Variant
probable methyltransferase TARBP1 isoform X8 XP_047285029.1:p.Leu534Phe L (Leu) > F (Phe) Missense Variant
TARBP1 transcript variant X10 XM_047429073.1:c.1600C>G L [CTT] > V [GTT] Coding Sequence Variant
probable methyltransferase TARBP1 isoform X8 XP_047285029.1:p.Leu534Val L (Leu) > V (Val) Missense Variant
TARBP1 transcript variant X11 XM_017002194.3:c.1600C>T L [CTT] > F [TTT] Coding Sequence Variant
probable methyltransferase TARBP1 isoform X9 XP_016857683.1:p.Leu534Phe L (Leu) > F (Phe) Missense Variant
TARBP1 transcript variant X11 XM_017002194.3:c.1600C>G L [CTT] > V [GTT] Coding Sequence Variant
probable methyltransferase TARBP1 isoform X9 XP_016857683.1:p.Leu534Val L (Leu) > V (Val) Missense Variant
TARBP1 transcript variant X12 XM_047429079.1:c.1600C>T L [CTT] > F [TTT] Coding Sequence Variant
probable methyltransferase TARBP1 isoform X10 XP_047285035.1:p.Leu534Phe L (Leu) > F (Phe) Missense Variant
TARBP1 transcript variant X12 XM_047429079.1:c.1600C>G L [CTT] > V [GTT] Coding Sequence Variant
probable methyltransferase TARBP1 isoform X10 XP_047285035.1:p.Leu534Val L (Leu) > V (Val) Missense Variant
TARBP1 transcript variant X13 XM_047429080.1:c.232C>T L [CTT] > F [TTT] Coding Sequence Variant
probable methyltransferase TARBP1 isoform X11 XP_047285036.1:p.Leu78Phe L (Leu) > F (Phe) Missense Variant
TARBP1 transcript variant X13 XM_047429080.1:c.232C>G L [CTT] > V [GTT] Coding Sequence Variant
probable methyltransferase TARBP1 isoform X11 XP_047285036.1:p.Leu78Val L (Leu) > V (Val) Missense Variant
TARBP1 transcript variant X15 XM_047429091.1:c.232C>T L [CTT] > F [TTT] Coding Sequence Variant
probable methyltransferase TARBP1 isoform X13 XP_047285047.1:p.Leu78Phe L (Leu) > F (Phe) Missense Variant
TARBP1 transcript variant X15 XM_047429091.1:c.232C>G L [CTT] > V [GTT] Coding Sequence Variant
probable methyltransferase TARBP1 isoform X13 XP_047285047.1:p.Leu78Val L (Leu) > V (Val) Missense Variant
TARBP1 transcript variant X5 XR_007063103.1:n.1676C>T N/A Non Coding Transcript Variant
TARBP1 transcript variant X5 XR_007063103.1:n.1676C>G N/A Non Coding Transcript Variant
TARBP1 transcript variant X6 XR_949157.3:n.1676C>T N/A Non Coding Transcript Variant
TARBP1 transcript variant X6 XR_949157.3:n.1676C>G 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.

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 G= A C
GRCh38.p14 chr 1 NC_000001.11:g.234459262= NC_000001.11:g.234459262G>A NC_000001.11:g.234459262G>C
GRCh37.p13 chr 1 NC_000001.10:g.234595008= NC_000001.10:g.234595008G>A NC_000001.10:g.234595008G>C
TARBP1 transcript NM_005646.4:c.1600= NM_005646.4:c.1600C>T NM_005646.4:c.1600C>G
TARBP1 transcript NM_005646.3:c.1600= NM_005646.3:c.1600C>T NM_005646.3:c.1600C>G
TARBP1 transcript variant X1 XM_005273234.4:c.1600= XM_005273234.4:c.1600C>T XM_005273234.4:c.1600C>G
TARBP1 transcript variant X1 XM_005273234.3:c.1600= XM_005273234.3:c.1600C>T XM_005273234.3:c.1600C>G
TARBP1 transcript variant X1 XM_005273234.2:c.1600= XM_005273234.2:c.1600C>T XM_005273234.2:c.1600C>G
TARBP1 transcript variant X1 XM_005273234.1:c.1600= XM_005273234.1:c.1600C>T XM_005273234.1:c.1600C>G
TARBP1 transcript variant X2 XM_011544263.3:c.1600= XM_011544263.3:c.1600C>T XM_011544263.3:c.1600C>G
TARBP1 transcript variant X2 XM_011544263.2:c.1600= XM_011544263.2:c.1600C>T XM_011544263.2:c.1600C>G
TARBP1 transcript variant X2 XM_011544263.1:c.1600= XM_011544263.1:c.1600C>T XM_011544263.1:c.1600C>G
TARBP1 transcript variant X6 XR_949157.3:n.1676= XR_949157.3:n.1676C>T XR_949157.3:n.1676C>G
TARBP1 transcript variant X7 XR_949157.2:n.1669= XR_949157.2:n.1669C>T XR_949157.2:n.1669C>G
TARBP1 transcript variant X5 XR_949157.1:n.1653= XR_949157.1:n.1653C>T XR_949157.1:n.1653C>G
TARBP1 transcript variant X11 XM_017002194.3:c.1600= XM_017002194.3:c.1600C>T XM_017002194.3:c.1600C>G
TARBP1 transcript variant X16 XM_017002194.2:c.1600= XM_017002194.2:c.1600C>T XM_017002194.2:c.1600C>G
TARBP1 transcript variant X14 XM_017002194.1:c.1600= XM_017002194.1:c.1600C>T XM_017002194.1:c.1600C>G
TARBP1 transcript variant X7 XM_047429067.1:c.1600= XM_047429067.1:c.1600C>T XM_047429067.1:c.1600C>G
TARBP1 transcript variant X8 XM_047429068.1:c.1600= XM_047429068.1:c.1600C>T XM_047429068.1:c.1600C>G
TARBP1 transcript variant X9 XM_047429072.1:c.1600= XM_047429072.1:c.1600C>T XM_047429072.1:c.1600C>G
TARBP1 transcript variant X3 XM_047429060.1:c.1600= XM_047429060.1:c.1600C>T XM_047429060.1:c.1600C>G
TARBP1 transcript variant X5 XR_007063103.1:n.1676= XR_007063103.1:n.1676C>T XR_007063103.1:n.1676C>G
TARBP1 transcript variant X15 XM_047429091.1:c.232= XM_047429091.1:c.232C>T XM_047429091.1:c.232C>G
TARBP1 transcript variant X4 XM_047429061.1:c.1600= XM_047429061.1:c.1600C>T XM_047429061.1:c.1600C>G
TARBP1 transcript variant X10 XM_047429073.1:c.1600= XM_047429073.1:c.1600C>T XM_047429073.1:c.1600C>G
TARBP1 transcript variant X13 XM_047429080.1:c.232= XM_047429080.1:c.232C>T XM_047429080.1:c.232C>G
TARBP1 transcript variant X12 XM_047429079.1:c.1600= XM_047429079.1:c.1600C>T XM_047429079.1:c.1600C>G
probable methyltransferase TARBP1 NP_005637.3:p.Leu534= NP_005637.3:p.Leu534Phe NP_005637.3:p.Leu534Val
probable methyltransferase TARBP1 isoform X1 XP_005273291.1:p.Leu534= XP_005273291.1:p.Leu534Phe XP_005273291.1:p.Leu534Val
probable methyltransferase TARBP1 isoform X2 XP_011542565.1:p.Leu534= XP_011542565.1:p.Leu534Phe XP_011542565.1:p.Leu534Val
probable methyltransferase TARBP1 isoform X9 XP_016857683.1:p.Leu534= XP_016857683.1:p.Leu534Phe XP_016857683.1:p.Leu534Val
probable methyltransferase TARBP1 isoform X5 XP_047285023.1:p.Leu534= XP_047285023.1:p.Leu534Phe XP_047285023.1:p.Leu534Val
probable methyltransferase TARBP1 isoform X6 XP_047285024.1:p.Leu534= XP_047285024.1:p.Leu534Phe XP_047285024.1:p.Leu534Val
probable methyltransferase TARBP1 isoform X7 XP_047285028.1:p.Leu534= XP_047285028.1:p.Leu534Phe XP_047285028.1:p.Leu534Val
probable methyltransferase TARBP1 isoform X3 XP_047285016.1:p.Leu534= XP_047285016.1:p.Leu534Phe XP_047285016.1:p.Leu534Val
probable methyltransferase TARBP1 isoform X13 XP_047285047.1:p.Leu78= XP_047285047.1:p.Leu78Phe XP_047285047.1:p.Leu78Val
probable methyltransferase TARBP1 isoform X4 XP_047285017.1:p.Leu534= XP_047285017.1:p.Leu534Phe XP_047285017.1:p.Leu534Val
probable methyltransferase TARBP1 isoform X8 XP_047285029.1:p.Leu534= XP_047285029.1:p.Leu534Phe XP_047285029.1:p.Leu534Val
probable methyltransferase TARBP1 isoform X11 XP_047285036.1:p.Leu78= XP_047285036.1:p.Leu78Phe XP_047285036.1:p.Leu78Val
probable methyltransferase TARBP1 isoform X10 XP_047285035.1:p.Leu534= XP_047285035.1:p.Leu534Phe XP_047285035.1:p.Leu534Val
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#.

4 SubSNP, 5 Frequency submissions
No Submitter Submission ID Date (Build)
1 GNOMAD ss2732372948 Nov 08, 2017 (151)
2 GNOMAD ss4013407447 Apr 25, 2021 (155)
3 TOPMED ss4487876501 Apr 25, 2021 (155)
4 TOPMED ss4487876502 Apr 25, 2021 (155)
5 gnomAD - Genomes NC_000001.11 - 234459262 Apr 25, 2021 (155)
6 gnomAD - Exomes NC_000001.10 - 234595008 Jul 12, 2019 (153)
7 TopMed

Submission ignored due to conflicting rows:
Row 51482836 (NC_000001.11:234459261:G:A 1/264690)
Row 51482837 (NC_000001.11:234459261:G:C 1/264690)

- Apr 25, 2021 (155)
8 TopMed

Submission ignored due to conflicting rows:
Row 51482836 (NC_000001.11:234459261:G:A 1/264690)
Row 51482837 (NC_000001.11:234459261:G:C 1/264690)

- Apr 25, 2021 (155)
9 ALFA NC_000001.11 - 234459262 Apr 25, 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
1410930, ss2732372948 NC_000001.10:234595007:G:A NC_000001.11:234459261:G:A (self)
1224994759, ss4487876501 NC_000001.11:234459261:G:A NC_000001.11:234459261:G:A (self)
43113245, 1224994759, ss4013407447, ss4487876502 NC_000001.11:234459261:G:C NC_000001.11:234459261:G:C (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 rs1486542868

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.post820+afb47a3d