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dbSNP Short Genetic Variations

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.

rs774658525

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr20:51799144-51799150 (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
delTAAA
Variation Type
Indel Insertion and Deletion
Frequency
delTAAA=0.000004 (1/264690, TOPMED)
delTAAA=0.000014 (2/140228, GnomAD)
delTAAA=0.00000 (0/14050, ALFA) (+ 2 more)
delTAAA=0.0003 (1/3854, ALSPAC)
delTAAA=0.0000 (0/3708, TWINSUK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
SALL4 : 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 14050 AAATAAA=1.00000 AAA=0.00000
European Sub 9690 AAATAAA=1.0000 AAA=0.0000
African Sub 2898 AAATAAA=1.0000 AAA=0.0000
African Others Sub 114 AAATAAA=1.000 AAA=0.000
African American Sub 2784 AAATAAA=1.0000 AAA=0.0000
Asian Sub 112 AAATAAA=1.000 AAA=0.000
East Asian Sub 86 AAATAAA=1.00 AAA=0.00
Other Asian Sub 26 AAATAAA=1.00 AAA=0.00
Latin American 1 Sub 146 AAATAAA=1.000 AAA=0.000
Latin American 2 Sub 610 AAATAAA=1.000 AAA=0.000
South Asian Sub 98 AAATAAA=1.00 AAA=0.00
Other Sub 496 AAATAAA=1.000 AAA=0.000


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 AAATAAA=0.999996 delTAAA=0.000004
gnomAD - Genomes Global Study-wide 140228 AAATAAA=0.999986 delTAAA=0.000014
gnomAD - Genomes European Sub 75936 AAATAAA=0.99997 delTAAA=0.00003
gnomAD - Genomes African Sub 42042 AAATAAA=1.00000 delTAAA=0.00000
gnomAD - Genomes American Sub 13644 AAATAAA=1.00000 delTAAA=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3324 AAATAAA=1.0000 delTAAA=0.0000
gnomAD - Genomes East Asian Sub 3134 AAATAAA=1.0000 delTAAA=0.0000
gnomAD - Genomes Other Sub 2148 AAATAAA=1.0000 delTAAA=0.0000
Allele Frequency Aggregator Total Global 14050 AAATAAA=1.00000 delTAAA=0.00000
Allele Frequency Aggregator European Sub 9690 AAATAAA=1.0000 delTAAA=0.0000
Allele Frequency Aggregator African Sub 2898 AAATAAA=1.0000 delTAAA=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 AAATAAA=1.000 delTAAA=0.000
Allele Frequency Aggregator Other Sub 496 AAATAAA=1.000 delTAAA=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 AAATAAA=1.000 delTAAA=0.000
Allele Frequency Aggregator Asian Sub 112 AAATAAA=1.000 delTAAA=0.000
Allele Frequency Aggregator South Asian Sub 98 AAATAAA=1.00 delTAAA=0.00
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 AAATAAA=0.9997 delTAAA=0.0003
UK 10K study - Twins TWIN COHORT Study-wide 3708 AAATAAA=1.0000 delTAAA=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 20 NC_000020.11:g.51799147_51799150del
GRCh37.p13 chr 20 NC_000020.10:g.50415686_50415689del
SALL4 RefSeqGene (LRG_675) NG_008000.1:g.8363_8366del
Gene: SALL4, spalt like transcription factor 4 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
SALL4 transcript variant 2 NM_001318031.2:c.130+3132…

NM_001318031.2:c.130+3132_130+3135del

N/A Intron Variant
SALL4 transcript variant 1 NM_020436.5:c.130+3132_13…

NM_020436.5:c.130+3132_130+3135del

N/A Intron Variant
SALL4 transcript variant X1 XM_047440318.1:c.-177+234…

XM_047440318.1:c.-177+2344_-177+2347del

N/A Intron 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 AAATAAA= delTAAA
GRCh38.p14 chr 20 NC_000020.11:g.51799144_51799150= NC_000020.11:g.51799147_51799150del
GRCh37.p13 chr 20 NC_000020.10:g.50415683_50415689= NC_000020.10:g.50415686_50415689del
SALL4 RefSeqGene (LRG_675) NG_008000.1:g.8360_8366= NG_008000.1:g.8363_8366del
SALL4 transcript variant 2 NM_001318031.2:c.130+3135= NM_001318031.2:c.130+3132_130+3135del
SALL4 transcript NM_020436.3:c.130+3135= NM_020436.3:c.130+3132_130+3135del
SALL4 transcript variant 1 NM_020436.5:c.130+3135= NM_020436.5:c.130+3132_130+3135del
SALL4 transcript variant X2 XM_005260468.1:c.130+3135= XM_005260468.1:c.130+3132_130+3135del
SALL4 transcript variant X1 XM_047440318.1:c.-177+2347= XM_047440318.1:c.-177+2344_-177+2347del
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 EVA_UK10K_ALSPAC ss1709392095 Apr 01, 2015 (144)
2 EVA_UK10K_TWINSUK ss1709392593 Apr 01, 2015 (144)
3 GNOMAD ss4354904916 Apr 27, 2021 (155)
4 TOPMED ss5091621208 Apr 27, 2021 (155)
5 The Avon Longitudinal Study of Parents and Children NC_000020.10 - 50415683 Oct 12, 2018 (152)
6 gnomAD - Genomes NC_000020.11 - 51799144 Apr 27, 2021 (155)
7 TopMed NC_000020.11 - 51799144 Apr 27, 2021 (155)
8 UK 10K study - Twins NC_000020.10 - 50415683 Oct 12, 2018 (152)
9 ALFA NC_000020.11 - 51799144 Apr 27, 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
43511678, 43511678, ss1709392095, ss1709392593 NC_000020.10:50415682:AAAT: NC_000020.11:51799143:AAATAAA:AAA (self)
554375521, 366730153, ss4354904916, ss5091621208 NC_000020.11:51799143:AAAT: NC_000020.11:51799143:AAATAAA:AAA (self)
7150571345 NC_000020.11:51799143:AAATAAA:AAA NC_000020.11:51799143:AAATAAA:AAA (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 rs774658525

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