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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.

rs1488664688

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr18:21449693 (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
T>C
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.000004 (1/264690, TOPMED)
C=0.000014 (2/140236, GnomAD)
C=0.00000 (0/14050, ALFA)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
GREB1L : Missense Variant
LOC101927521 : 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: 20231103111315
Population Group Sample Size Ref Allele Alt Allele Ref HMOZ Alt HMOZ HTRZ HWEP
Total Global 14050 T=1.00000 C=0.00000 1.0 0.0 0.0 N/A
European Sub 9690 T=1.0000 C=0.0000 1.0 0.0 0.0 N/A
African Sub 2898 T=1.0000 C=0.0000 1.0 0.0 0.0 N/A
African Others Sub 114 T=1.000 C=0.000 1.0 0.0 0.0 N/A
African American Sub 2784 T=1.0000 C=0.0000 1.0 0.0 0.0 N/A
Asian Sub 112 T=1.000 C=0.000 1.0 0.0 0.0 N/A
East Asian Sub 86 T=1.00 C=0.00 1.0 0.0 0.0 N/A
Other Asian Sub 26 T=1.00 C=0.00 1.0 0.0 0.0 N/A
Latin American 1 Sub 146 T=1.000 C=0.000 1.0 0.0 0.0 N/A
Latin American 2 Sub 610 T=1.000 C=0.000 1.0 0.0 0.0 N/A
South Asian Sub 98 T=1.00 C=0.00 1.0 0.0 0.0 N/A
Other Sub 496 T=1.000 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
TopMed Global Study-wide 264690 T=0.999996 C=0.000004
gnomAD - Genomes Global Study-wide 140236 T=0.999986 C=0.000014
gnomAD - Genomes European Sub 75940 T=0.99997 C=0.00003
gnomAD - Genomes African Sub 42036 T=1.00000 C=0.00000
gnomAD - Genomes American Sub 13656 T=1.00000 C=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3322 T=1.0000 C=0.0000
gnomAD - Genomes East Asian Sub 3130 T=1.0000 C=0.0000
gnomAD - Genomes Other Sub 2152 T=1.0000 C=0.0000
Allele Frequency Aggregator Total Global 14050 T=1.00000 C=0.00000
Allele Frequency Aggregator European Sub 9690 T=1.0000 C=0.0000
Allele Frequency Aggregator African Sub 2898 T=1.0000 C=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 T=1.000 C=0.000
Allele Frequency Aggregator Other Sub 496 T=1.000 C=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 T=1.000 C=0.000
Allele Frequency Aggregator Asian Sub 112 T=1.000 C=0.000
Allele Frequency Aggregator South Asian Sub 98 T=1.00 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 18 NC_000018.10:g.21449693T>C
GRCh37.p13 chr 18 NC_000018.9:g.19029654T>C
Gene: GREB1L, GREB1 like retinoic acid receptor coactivator (plus strand)
Molecule type Change Amino acid[Codon] SO Term
GREB1L transcript variant 2 NM_001142966.3:c.1577T>C V [GTG] > A [GCG] Coding Sequence Variant
GREB1-like protein isoform 2 NP_001136438.1:p.Val526Ala V (Val) > A (Ala) Missense Variant
GREB1L transcript variant X17 XM_017025994.2:c.1523-133…

XM_017025994.2:c.1523-1330T>C

 		N/A Intron Variant
GREB1L transcript variant X19 XM_017025995.2:c.1523-133…

XM_017025995.2:c.1523-1330T>C

 		N/A Intron Variant
GREB1L transcript variant X21 XM_017025996.2:c.1394-133…

XM_017025996.2:c.1394-1330T>C

 		N/A Intron Variant
GREB1L transcript variant X18 XM_047437820.1:c.1523-133…

XM_047437820.1:c.1523-1330T>C

 		N/A Intron Variant
GREB1L transcript variant X22 XM_047437822.1:c.1394-133…

XM_047437822.1:c.1394-1330T>C

 		N/A Intron Variant
GREB1L transcript variant X24 XM_047437823.1:c.1394-133…

XM_047437823.1:c.1394-1330T>C

 		N/A Intron Variant
GREB1L transcript variant X25 XM_047437826.1:c.1523-133…

XM_047437826.1:c.1523-1330T>C

 		N/A Intron Variant
GREB1L transcript variant X26 XM_047437827.1:c.1394-133…

XM_047437827.1:c.1394-1330T>C

 		N/A Intron Variant
GREB1L transcript variant X1 XM_047437809.1:c.1706T>C V [GTG] > A [GCG] Coding Sequence Variant
GREB1-like protein isoform X1 XP_047293765.1:p.Val569Ala V (Val) > A (Ala) Missense Variant
GREB1L transcript variant X2 XM_047437810.1:c.1706T>C V [GTG] > A [GCG] Coding Sequence Variant
GREB1-like protein isoform X1 XP_047293766.1:p.Val569Ala V (Val) > A (Ala) Missense Variant
GREB1L transcript variant X3 XM_017025989.2:c.1706T>C V [GTG] > A [GCG] Coding Sequence Variant
GREB1-like protein isoform X1 XP_016881478.1:p.Val569Ala V (Val) > A (Ala) Missense Variant
GREB1L transcript variant X4 XM_017025990.2:c.1706T>C V [GTG] > A [GCG] Coding Sequence Variant
GREB1-like protein isoform X2 XP_016881479.1:p.Val569Ala V (Val) > A (Ala) Missense Variant
GREB1L transcript variant X5 XM_017025991.2:c.1706T>C V [GTG] > A [GCG] Coding Sequence Variant
GREB1-like protein isoform X3 XP_016881480.1:p.Val569Ala V (Val) > A (Ala) Missense Variant
GREB1L transcript variant X6 XM_047437811.1:c.1706T>C V [GTG] > A [GCG] Coding Sequence Variant
GREB1-like protein isoform X4 XP_047293767.1:p.Val569Ala V (Val) > A (Ala) Missense Variant
GREB1L transcript variant X7 XM_006722547.4:c.1706T>C V [GTG] > A [GCG] Coding Sequence Variant
GREB1-like protein isoform X5 XP_006722610.1:p.Val569Ala V (Val) > A (Ala) Missense Variant
GREB1L transcript variant X8 XM_047437812.1:c.1706T>C V [GTG] > A [GCG] Coding Sequence Variant
GREB1-like protein isoform X6 XP_047293768.1:p.Val569Ala V (Val) > A (Ala) Missense Variant
GREB1L transcript variant X8 XM_047437813.1:c.1577T>C V [GTG] > A [GCG] Coding Sequence Variant
GREB1-like protein isoform X6 XP_047293769.1:p.Val526Ala V (Val) > A (Ala) Missense Variant
GREB1L transcript variant X9 XM_017025993.2:c.1577T>C V [GTG] > A [GCG] Coding Sequence Variant
GREB1-like protein isoform X6 XP_016881482.1:p.Val526Ala V (Val) > A (Ala) Missense Variant
GREB1L transcript variant X10 XM_047437814.1:c.1577T>C V [GTG] > A [GCG] Coding Sequence Variant
GREB1-like protein isoform X6 XP_047293770.1:p.Val526Ala V (Val) > A (Ala) Missense Variant
GREB1L transcript variant X11 XM_047437815.1:c.1577T>C V [GTG] > A [GCG] Coding Sequence Variant
GREB1-like protein isoform X7 XP_047293771.1:p.Val526Ala V (Val) > A (Ala) Missense Variant
GREB1L transcript variant X12 XM_047437816.1:c.1706T>C V [GTG] > A [GCG] Coding Sequence Variant
GREB1-like protein isoform X8 XP_047293772.1:p.Val569Ala V (Val) > A (Ala) Missense Variant
GREB1L transcript variant X13 XM_047437817.1:c.1577T>C V [GTG] > A [GCG] Coding Sequence Variant
GREB1-like protein isoform X9 XP_047293773.1:p.Val526Ala V (Val) > A (Ala) Missense Variant
GREB1L transcript variant X14 XM_047437818.1:c.1577T>C V [GTG] > A [GCG] Coding Sequence Variant
GREB1-like protein isoform X10 XP_047293774.1:p.Val526Ala V (Val) > A (Ala) Missense Variant
GREB1L transcript variant X15 XM_047437819.1:c.1577T>C V [GTG] > A [GCG] Coding Sequence Variant
GREB1-like protein isoform X10 XP_047293775.1:p.Val526Ala V (Val) > A (Ala) Missense Variant
GREB1L transcript variant X16 XM_011526179.4:c.1706T>C V [GTG] > A [GCG] Coding Sequence Variant
GREB1-like protein isoform X11 XP_011524481.1:p.Val569Ala V (Val) > A (Ala) Missense Variant
GREB1L transcript variant X20 XM_047437821.1:c.1577T>C V [GTG] > A [GCG] Coding Sequence Variant
GREB1-like protein isoform X14 XP_047293777.1:p.Val526Ala V (Val) > A (Ala) Missense Variant
GREB1L transcript variant X23 XM_047437824.1:c.1577T>C V [GTG] > A [GCG] Coding Sequence Variant
GREB1-like protein isoform X16 XP_047293780.1:p.Val526Ala V (Val) > A (Ala) Missense Variant
GREB1L transcript variant X24 XM_047437825.1:c.1577T>C V [GTG] > A [GCG] Coding Sequence Variant
GREB1-like protein isoform X17 XP_047293781.1:p.Val526Ala V (Val) > A (Ala) Missense Variant
Gene: LOC101927521, uncharacterized LOC101927521 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
LOC101927521 transcript variant X2 XR_001753366.2:n. N/A Intron Variant
LOC101927521 transcript variant X1 XR_935272.3:n. N/A Intron Variant
LOC101927521 transcript variant X3 XR_001753367.2:n. N/A Genic Upstream 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 T= C
GRCh38.p14 chr 18 NC_000018.10:g.21449693= NC_000018.10:g.21449693T>C
GRCh37.p13 chr 18 NC_000018.9:g.19029654= NC_000018.9:g.19029654T>C
GREB1L transcript variant X7 XM_006722547.4:c.1706= XM_006722547.4:c.1706T>C
GREB1L transcript variant X5 XM_006722547.3:c.1706= XM_006722547.3:c.1706T>C
GREB1L transcript variant X5 XM_006722547.2:c.1706= XM_006722547.2:c.1706T>C
GREB1L transcript variant X1 XM_006722547.1:c.1706= XM_006722547.1:c.1706T>C
GREB1L transcript variant X16 XM_011526179.4:c.1706= XM_011526179.4:c.1706T>C
GREB1L transcript variant X8 XM_011526179.3:c.1706= XM_011526179.3:c.1706T>C
GREB1L transcript variant X8 XM_011526179.2:c.1706= XM_011526179.2:c.1706T>C
GREB1L transcript variant X5 XM_011526179.1:c.1706= XM_011526179.1:c.1706T>C
GREB1L transcript variant 2 NM_001142966.3:c.1577= NM_001142966.3:c.1577T>C
GREB1L transcript NM_001142966.2:c.1577= NM_001142966.2:c.1577T>C
GREB1L transcript NM_001142966.1:c.1577= NM_001142966.1:c.1577T>C
GREB1L transcript variant X4 XM_017025990.2:c.1706= XM_017025990.2:c.1706T>C
GREB1L transcript variant X3 XM_017025990.1:c.1706= XM_017025990.1:c.1706T>C
GREB1L transcript variant X5 XM_017025991.2:c.1706= XM_017025991.2:c.1706T>C
GREB1L transcript variant X4 XM_017025991.1:c.1706= XM_017025991.1:c.1706T>C
GREB1L transcript variant X3 XM_017025989.2:c.1706= XM_017025989.2:c.1706T>C
GREB1L transcript variant X2 XM_017025989.1:c.1706= XM_017025989.1:c.1706T>C
GREB1L transcript variant X9 XM_017025993.2:c.1577= XM_017025993.2:c.1577T>C
GREB1L transcript variant X7 XM_017025993.1:c.1577= XM_017025993.1:c.1577T>C
KIAA1772 transcript NM_024935.2:c.1577= NM_024935.2:c.1577T>C
GREB1L transcript variant X8 XM_047437812.1:c.1706= XM_047437812.1:c.1706T>C
GREB1L transcript variant 1 NM_001410867.1:c.1706= NM_001410867.1:c.1706T>C
GREB1L transcript variant X12 XM_047437816.1:c.1706= XM_047437816.1:c.1706T>C
GREB1L transcript variant X15 XM_047437819.1:c.1577= XM_047437819.1:c.1577T>C
GREB1L transcript variant X14 XM_047437818.1:c.1577= XM_047437818.1:c.1577T>C
GREB1L transcript variant X20 XM_047437821.1:c.1577= XM_047437821.1:c.1577T>C
GREB1L transcript variant X2 XM_047437810.1:c.1706= XM_047437810.1:c.1706T>C
GREB1L transcript variant X1 XM_047437809.1:c.1706= XM_047437809.1:c.1706T>C
GREB1L transcript variant X10 XM_047437814.1:c.1577= XM_047437814.1:c.1577T>C
GREB1L transcript variant X6 XM_047437811.1:c.1706= XM_047437811.1:c.1706T>C
GREB1L transcript variant X8 XM_047437813.1:c.1577= XM_047437813.1:c.1577T>C
GREB1L transcript variant X11 XM_047437815.1:c.1577= XM_047437815.1:c.1577T>C
GREB1L transcript variant X13 XM_047437817.1:c.1577= XM_047437817.1:c.1577T>C
GREB1L transcript variant X23 XM_047437824.1:c.1577= XM_047437824.1:c.1577T>C
GREB1L transcript variant X24 XM_047437825.1:c.1577= XM_047437825.1:c.1577T>C
GREB1-like protein isoform X5 XP_006722610.1:p.Val569= XP_006722610.1:p.Val569Ala
GREB1-like protein isoform X11 XP_011524481.1:p.Val569= XP_011524481.1:p.Val569Ala
GREB1-like protein isoform 2 NP_001136438.1:p.Val526= NP_001136438.1:p.Val526Ala
GREB1-like protein isoform X2 XP_016881479.1:p.Val569= XP_016881479.1:p.Val569Ala
GREB1-like protein isoform X3 XP_016881480.1:p.Val569= XP_016881480.1:p.Val569Ala
GREB1-like protein isoform X1 XP_016881478.1:p.Val569= XP_016881478.1:p.Val569Ala
GREB1-like protein isoform X6 XP_016881482.1:p.Val526= XP_016881482.1:p.Val526Ala
GREB1-like protein isoform X6 XP_047293768.1:p.Val569= XP_047293768.1:p.Val569Ala
GREB1-like protein isoform X8 XP_047293772.1:p.Val569= XP_047293772.1:p.Val569Ala
GREB1-like protein isoform X10 XP_047293775.1:p.Val526= XP_047293775.1:p.Val526Ala
GREB1-like protein isoform X10 XP_047293774.1:p.Val526= XP_047293774.1:p.Val526Ala
GREB1-like protein isoform X14 XP_047293777.1:p.Val526= XP_047293777.1:p.Val526Ala
GREB1-like protein isoform X1 XP_047293766.1:p.Val569= XP_047293766.1:p.Val569Ala
GREB1-like protein isoform X1 XP_047293765.1:p.Val569= XP_047293765.1:p.Val569Ala
GREB1-like protein isoform X6 XP_047293770.1:p.Val526= XP_047293770.1:p.Val526Ala
GREB1-like protein isoform X4 XP_047293767.1:p.Val569= XP_047293767.1:p.Val569Ala
GREB1-like protein isoform X6 XP_047293769.1:p.Val526= XP_047293769.1:p.Val526Ala
GREB1-like protein isoform X7 XP_047293771.1:p.Val526= XP_047293771.1:p.Val526Ala
GREB1-like protein isoform X9 XP_047293773.1:p.Val526= XP_047293773.1:p.Val526Ala
GREB1-like protein isoform X16 XP_047293780.1:p.Val526= XP_047293780.1:p.Val526Ala
GREB1-like protein isoform X17 XP_047293781.1:p.Val526= XP_047293781.1:p.Val526Ala
GREB1L transcript variant X17 XM_017025994.2:c.1523-1330= XM_017025994.2:c.1523-1330T>C
GREB1L transcript variant X19 XM_017025995.2:c.1523-1330= XM_017025995.2:c.1523-1330T>C
GREB1L transcript variant X21 XM_017025996.2:c.1394-1330= XM_017025996.2:c.1394-1330T>C
GREB1L transcript variant X18 XM_047437820.1:c.1523-1330= XM_047437820.1:c.1523-1330T>C
GREB1L transcript variant X22 XM_047437822.1:c.1394-1330= XM_047437822.1:c.1394-1330T>C
GREB1L transcript variant X24 XM_047437823.1:c.1394-1330= XM_047437823.1:c.1394-1330T>C
GREB1L transcript variant X25 XM_047437826.1:c.1523-1330= XM_047437826.1:c.1523-1330T>C
GREB1L transcript variant X26 XM_047437827.1:c.1394-1330= XM_047437827.1:c.1394-1330T>C
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#.

2 SubSNP, 3 Frequency submissions
No Submitter Submission ID Date (Build)
1 GNOMAD ss4318815196 Apr 26, 2021 (155)
2 TOPMED ss5050120071 Apr 26, 2021 (155)
3 gnomAD - Genomes NC_000018.10 - 21449693 Apr 26, 2021 (155)
4 TopMed NC_000018.10 - 21449693 Apr 26, 2021 (155)
5 ALFA NC_000018.10 - 21449693 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
519187865, 265665734, 2369363939, ss4318815196, ss5050120071 NC_000018.10:21449692:T:C NC_000018.10:21449692:T: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 rs1488664688

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