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dbSNP Short Genetic Variations

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.

rs1057517403

Current Build 152

Released October 2, 2018

Organism
Homo sapiens
Position
chr17:19649122-19649123 (GRCh38.p12) 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
delAA
Variation Type
Deletion
Frequency
delAA=0.00001 (1/125568, TOPMED)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
ALDH3A2 : Frameshift
Publications
0 citations
Genomic View
See rs on genome
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.p12 chr 17 NC_000017.11:g.19649122_19649123delAA
GRCh37.p13 chr 17 NC_000017.10:g.19552435_19552436delAA
ALDH3A2 RefSeqGene NG_007095.2:g.5372_5373delAA
Gene: ALDH3A2, aldehyde dehydrogenase 3 family member A2 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
ALDH3A2 transcript variant 2 NM_000382.2:c.151_152delAA K [AA] > E [G] Coding Sequence Variant
fatty aldehyde dehydrogenase isoform 2 NP_000373.1:p.Lys51fs K (Lys) > E (Glu) Frameshift
ALDH3A2 transcript variant 1 NM_001031806.1:c.151_15...

NM_001031806.1:c.151_152delAA

K [AA] > E [G] Coding Sequence Variant
fatty aldehyde dehydrogenase isoform 1 NP_001026976.1:p.Lys51fs K (Lys) > E (Glu) Frameshift
ALDH3A2 transcript variant X8 XM_024450652.1:c. N/A 5 Prime UTR Variant
ALDH3A2 transcript variant X7 XM_024450651.1:c. N/A Genic Upstream Transcript Variant
ALDH3A2 transcript variant X1 XM_011523732.1:c.151_15...

XM_011523732.1:c.151_152delAA

K [AA] > E [G] Coding Sequence Variant
fatty aldehyde dehydrogenase isoform X1 XP_011522034.1:p.Lys51fs K (Lys) > E (Glu) Frameshift
ALDH3A2 transcript variant X3 XM_017024355.1:c.151_15...

XM_017024355.1:c.151_152delAA

K [AA] > E [G] Coding Sequence Variant
fatty aldehyde dehydrogenase isoform X2 XP_016879844.1:p.Lys51fs K (Lys) > E (Glu) Frameshift
ALDH3A2 transcript variant X5 XM_017024357.1:c.151_15...

XM_017024357.1:c.151_152delAA

K [AA] > E [G] Coding Sequence Variant
fatty aldehyde dehydrogenase isoform X3 XP_016879846.1:p.Lys51fs K (Lys) > E (Glu) Frameshift
ALDH3A2 transcript variant X2 XM_011523733.2:c.151_15...

XM_011523733.2:c.151_152delAA

K [AA] > E [G] Coding Sequence Variant
fatty aldehyde dehydrogenase isoform X1 XP_011522035.1:p.Lys51fs K (Lys) > E (Glu) Frameshift
ALDH3A2 transcript variant X4 XM_017024356.2:c.151_15...

XM_017024356.2:c.151_152delAA

K [AA] > E [G] Coding Sequence Variant
fatty aldehyde dehydrogenase isoform X3 XP_016879845.1:p.Lys51fs K (Lys) > E (Glu) Frameshift
ALDH3A2 transcript variant X6 XM_017024358.2:c.151_15...

XM_017024358.2:c.151_152delAA

K [AA] > E [G] Coding Sequence Variant
fatty aldehyde dehydrogenase isoform X2 XP_016879847.1:p.Lys51fs K (Lys) > E (Glu) Frameshift
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

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 125568 AA=0.99999 delAA=0.00001
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 AA= delAA Note
GRCh38.p12 chr 17 NC_000017.11:g.19649122...

NC_000017.11:g.19649122_19649123AA=

NC_000017.11:g.19649122...

NC_000017.11:g.19649122_19649123delAA

GRCh37.p13 chr 17 NC_000017.10:g.19552435...

NC_000017.10:g.19552435_19552436AA=

NC_000017.10:g.19552435...

NC_000017.10:g.19552435_19552436delAA

ALDH3A2 RefSeqGene NG_007095.2:g.5372_5373AA= NG_007095.2:g.5372_5373...

NG_007095.2:g.5372_5373delAA

ALDH3A2 transcript variant 2 NM_000382.2:c.151_152AA= NM_000382.2:c.151_152delAA
ALDH3A2 transcript variant 1 NM_001031806.1:c.151_15...

NM_001031806.1:c.151_152AA=

NM_001031806.1:c.151_15...

NM_001031806.1:c.151_152delAA

ALDH3A2 transcript variant X2 XM_011523733.2:c.151_15...

XM_011523733.2:c.151_152AA=

XM_011523733.2:c.151_15...

XM_011523733.2:c.151_152delAA

ALDH3A2 transcript variant X4 XM_017024356.2:c.151_15...

XM_017024356.2:c.151_152AA=

XM_017024356.2:c.151_15...

XM_017024356.2:c.151_152delAA

ALDH3A2 transcript variant X6 XM_017024358.2:c.151_15...

XM_017024358.2:c.151_152AA=

XM_017024358.2:c.151_15...

XM_017024358.2:c.151_152delAA

ALDH3A2 transcript variant X1 XM_011523732.1:c.151_15...

XM_011523732.1:c.151_152AA=

XM_011523732.1:c.151_15...

XM_011523732.1:c.151_152delAA

ALDH3A2 transcript variant X8 XM_024450652.1:c.-538_-...

XM_024450652.1:c.-538_-537AA=

XM_024450652.1:c.-538_-...

XM_024450652.1:c.-538_-537delAA

ALDH3A2 transcript variant X5 XM_017024357.1:c.151_15...

XM_017024357.1:c.151_152AA=

XM_017024357.1:c.151_15...

XM_017024357.1:c.151_152delAA

ALDH3A2 transcript variant X3 XM_017024355.1:c.151_15...

XM_017024355.1:c.151_152AA=

XM_017024355.1:c.151_15...

XM_017024355.1:c.151_152delAA

fatty aldehyde dehydrogenase isoform 2 NP_000373.1:p.Lys51= NP_000373.1:p.Lys51fs
fatty aldehyde dehydrogenase isoform 1 NP_001026976.1:p.Lys51= NP_001026976.1:p.Lys51fs
fatty aldehyde dehydrogenase isoform X1 XP_011522035.1:p.Lys51= XP_011522035.1:p.Lys51fs
fatty aldehyde dehydrogenase isoform X3 XP_016879845.1:p.Lys51= XP_016879845.1:p.Lys51fs
fatty aldehyde dehydrogenase isoform X2 XP_016879847.1:p.Lys51= XP_016879847.1:p.Lys51fs
fatty aldehyde dehydrogenase isoform X1 XP_011522034.1:p.Lys51= XP_011522034.1:p.Lys51fs
fatty aldehyde dehydrogenase isoform X3 XP_016879846.1:p.Lys51= XP_016879846.1:p.Lys51fs
fatty aldehyde dehydrogenase isoform X2 XP_016879844.1:p.Lys51= XP_016879844.1:p.Lys51fs
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, 1 Frequency submissions
No Submitter Submission ID Date (Build)
1 CLINVAR ss2137339433 Jan 09, 2017 (149)
2 TOPMED ss3258946673 Nov 08, 2017 (151)
3 TopMed NC_000017.11 - 19649122 Oct 12, 2018 (152)
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
154252584, ss2137339433, ss3258946673 NC_000017.11:19649121:AA= NC_000017.11:19649121:AA= (self)
154252584, ss2137339433, ss3258946673 NC_000017.11:19649121:delAA NC_000017.11:19649121:delAA (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 rs1057517403

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.post63+3f7b20b