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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.

rs1491469748

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr14:54684613-54684614 (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
insG / insT
Variation Type
Insertion
Frequency
insT=0.00002 (1/44636, GnomAD)
insG=0.00000 (0/11862, ALFA)
insT=0.00000 (0/11862, ALFA)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
SAMD4A-AS1 : Non Coding Transcript Variant
SAMD4A : 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 11862 =1.00000 G=0.00000, T=0.00000 1.0 0.0 0.0 N/A
European Sub 7618 =1.0000 G=0.0000, T=0.0000 1.0 0.0 0.0 N/A
African Sub 2816 =1.0000 G=0.0000, T=0.0000 1.0 0.0 0.0 N/A
African Others Sub 108 =1.000 G=0.000, T=0.000 1.0 0.0 0.0 N/A
African American Sub 2708 =1.0000 G=0.0000, T=0.0000 1.0 0.0 0.0 N/A
Asian Sub 108 =1.000 G=0.000, T=0.000 1.0 0.0 0.0 N/A
East Asian Sub 84 =1.00 G=0.00, T=0.00 1.0 0.0 0.0 N/A
Other Asian Sub 24 =1.00 G=0.00, T=0.00 1.0 0.0 0.0 N/A
Latin American 1 Sub 146 =1.000 G=0.000, T=0.000 1.0 0.0 0.0 N/A
Latin American 2 Sub 610 =1.000 G=0.000, T=0.000 1.0 0.0 0.0 N/A
South Asian Sub 94 =1.00 G=0.00, T=0.00 1.0 0.0 0.0 N/A
Other Sub 470 =1.000 G=0.000, T=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 - Genomes Global Study-wide 44636 -

No frequency provided

insT=0.00002
gnomAD - Genomes African Sub 19348 -

No frequency provided

insT=0.00005
gnomAD - Genomes European Sub 16348 -

No frequency provided

insT=0.00000
gnomAD - Genomes American Sub 5282 -

No frequency provided

insT=0.0000
gnomAD - Genomes East Asian Sub 1650 -

No frequency provided

insT=0.0000
gnomAD - Genomes Ashkenazi Jewish Sub 1232 -

No frequency provided

insT=0.0000
gnomAD - Genomes Other Sub 776 -

No frequency provided

insT=0.000
Allele Frequency Aggregator Total Global 11862 -

No frequency provided

insG=0.00000, insT=0.00000
Allele Frequency Aggregator European Sub 7618 -

No frequency provided

insG=0.0000, insT=0.0000
Allele Frequency Aggregator African Sub 2816 -

No frequency provided

insG=0.0000, insT=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 -

No frequency provided

insG=0.000, insT=0.000
Allele Frequency Aggregator Other Sub 470 -

No frequency provided

insG=0.000, insT=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 -

No frequency provided

insG=0.000, insT=0.000
Allele Frequency Aggregator Asian Sub 108 -

No frequency provided

insG=0.000, insT=0.000
Allele Frequency Aggregator South Asian Sub 94 -

No frequency provided

insG=0.00, insT=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 14 NC_000014.9:g.54684613_54684614insG
GRCh38.p14 chr 14 NC_000014.9:g.54684613_54684614insT
GRCh37.p13 chr 14 NC_000014.8:g.55151331_55151332insG
GRCh37.p13 chr 14 NC_000014.8:g.55151331_55151332insT
Gene: SAMD4A, sterile alpha motif domain containing 4A (plus strand)
Molecule type Change Amino acid[Codon] SO Term
SAMD4A transcript variant 2 NM_001161576.2:c.197-1744…

NM_001161576.2:c.197-17449_197-17448insG

N/A Intron Variant
SAMD4A transcript variant 1 NM_015589.6:c.197-17449_1…

NM_015589.6:c.197-17449_197-17448insG

N/A Intron Variant
SAMD4A transcript variant 3 NM_001161577.2:c. N/A Genic Upstream Transcript Variant
SAMD4A transcript variant X2 XM_024449514.2:c.197-1744…

XM_024449514.2:c.197-17449_197-17448insG

N/A Intron Variant
SAMD4A transcript variant X3 XM_024449515.2:c.197-1744…

XM_024449515.2:c.197-17449_197-17448insG

N/A Intron Variant
SAMD4A transcript variant X5 XM_024449516.2:c.197-1744…

XM_024449516.2:c.197-17449_197-17448insG

N/A Intron Variant
SAMD4A transcript variant X1 XM_047431136.1:c.197-1744…

XM_047431136.1:c.197-17449_197-17448insG

N/A Intron Variant
SAMD4A transcript variant X4 XM_047431137.1:c.197-1744…

XM_047431137.1:c.197-17449_197-17448insG

N/A Intron Variant
SAMD4A transcript variant X6 XM_047431138.1:c.197-1744…

XM_047431138.1:c.197-17449_197-17448insG

N/A Intron Variant
SAMD4A transcript variant X7 XM_047431139.1:c.197-1744…

XM_047431139.1:c.197-17449_197-17448insG

N/A Intron Variant
SAMD4A transcript variant X8 XM_047431140.1:c.197-1744…

XM_047431140.1:c.197-17449_197-17448insG

N/A Intron Variant
SAMD4A transcript variant X9 XM_047431141.1:c.197-1744…

XM_047431141.1:c.197-17449_197-17448insG

N/A Intron Variant
SAMD4A transcript variant X10 XM_047431142.1:c.-108+255…

XM_047431142.1:c.-108+2556_-108+2557insG

N/A Intron Variant
SAMD4A transcript variant X11 XM_047431143.1:c.197-1744…

XM_047431143.1:c.197-17449_197-17448insG

N/A Intron Variant
SAMD4A transcript variant X12 XM_047431144.1:c.197-1744…

XM_047431144.1:c.197-17449_197-17448insG

N/A Intron Variant
SAMD4A transcript variant X13 XM_047431145.1:c.197-1744…

XM_047431145.1:c.197-17449_197-17448insG

N/A Intron Variant
SAMD4A transcript variant X14 XM_047431146.1:c.197-1744…

XM_047431146.1:c.197-17449_197-17448insG

N/A Intron Variant
Gene: SAMD4A-AS1, uncharacterized SAMD4A-AS1 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
SAMD4A-AS1 transcript variant X1 XR_429363.5:n.798_799insC N/A Non Coding Transcript Variant
SAMD4A-AS1 transcript variant X1 XR_429363.5:n.798_799insA N/A Non Coding Transcript Variant
SAMD4A-AS1 transcript variant X2 XR_943885.4:n.782_783insC N/A Non Coding Transcript Variant
SAMD4A-AS1 transcript variant X2 XR_943885.4:n.782_783insA N/A Non Coding Transcript Variant
SAMD4A-AS1 transcript variant X3 XR_943887.2:n.1493_1494in…

XR_943887.2:n.1493_1494insC

N/A Non Coding Transcript Variant
SAMD4A-AS1 transcript variant X3 XR_943887.2:n.1493_1494in…

XR_943887.2:n.1493_1494insA

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 = insG insT
GRCh38.p14 chr 14 NC_000014.9:g.54684613_54684614= NC_000014.9:g.54684613_54684614insG NC_000014.9:g.54684613_54684614insT
GRCh37.p13 chr 14 NC_000014.8:g.55151331_55151332= NC_000014.8:g.55151331_55151332insG NC_000014.8:g.55151331_55151332insT
SAMD4A-AS1 transcript variant X1 XR_429363.5:n.798_799= XR_429363.5:n.798_799insC XR_429363.5:n.798_799insA
LOC729451 transcript variant X1 XR_429363.4:n.1134_1135= XR_429363.4:n.1134_1135insC XR_429363.4:n.1134_1135insA
LOC729451 transcript variant X1 XR_429363.3:n.1088_1089= XR_429363.3:n.1088_1089insC XR_429363.3:n.1088_1089insA
LOC729451 transcript variant X1 XR_429363.2:n.1146_1147= XR_429363.2:n.1146_1147insC XR_429363.2:n.1146_1147insA
SAMD4A-AS1 transcript variant X2 XR_943885.4:n.782_783= XR_943885.4:n.782_783insC XR_943885.4:n.782_783insA
LOC729451 transcript variant X2 XR_943885.3:n.1102_1103= XR_943885.3:n.1102_1103insC XR_943885.3:n.1102_1103insA
LOC729451 transcript variant X2 XR_943885.2:n.1072_1073= XR_943885.2:n.1072_1073insC XR_943885.2:n.1072_1073insA
LOC729451 transcript variant X2 XR_943885.1:n.1124_1125= XR_943885.1:n.1124_1125insC XR_943885.1:n.1124_1125insA
SAMD4A-AS1 transcript variant X3 XR_943887.2:n.1493_1494= XR_943887.2:n.1493_1494insC XR_943887.2:n.1493_1494insA
LOC729451 transcript variant X3 XR_943887.1:n.1493_1494= XR_943887.1:n.1493_1494insC XR_943887.1:n.1493_1494insA
SAMD4A transcript variant 2 NM_001161576.2:c.197-17448= NM_001161576.2:c.197-17449_197-17448insG NM_001161576.2:c.197-17449_197-17448insT
SAMD4A transcript variant 1 NM_015589.5:c.197-17448= NM_015589.5:c.197-17449_197-17448insG NM_015589.5:c.197-17449_197-17448insT
SAMD4A transcript variant 1 NM_015589.6:c.197-17448= NM_015589.6:c.197-17449_197-17448insG NM_015589.6:c.197-17449_197-17448insT
SAMD4A transcript variant X1 XM_005267432.1:c.197-17448= XM_005267432.1:c.197-17449_197-17448insG XM_005267432.1:c.197-17449_197-17448insT
SAMD4A transcript variant X2 XM_005267433.1:c.197-17448= XM_005267433.1:c.197-17449_197-17448insG XM_005267433.1:c.197-17449_197-17448insT
SAMD4A transcript variant X4 XM_005267435.1:c.197-17448= XM_005267435.1:c.197-17449_197-17448insG XM_005267435.1:c.197-17449_197-17448insT
SAMD4A transcript variant X6 XM_005267437.1:c.-108+2557= XM_005267437.1:c.-108+2556_-108+2557insG XM_005267437.1:c.-108+2556_-108+2557insT
SAMD4A transcript variant X2 XM_024449514.2:c.197-17448= XM_024449514.2:c.197-17449_197-17448insG XM_024449514.2:c.197-17449_197-17448insT
SAMD4A transcript variant X3 XM_024449515.2:c.197-17448= XM_024449515.2:c.197-17449_197-17448insG XM_024449515.2:c.197-17449_197-17448insT
SAMD4A transcript variant X5 XM_024449516.2:c.197-17448= XM_024449516.2:c.197-17449_197-17448insG XM_024449516.2:c.197-17449_197-17448insT
SAMD4A transcript variant X1 XM_047431136.1:c.197-17448= XM_047431136.1:c.197-17449_197-17448insG XM_047431136.1:c.197-17449_197-17448insT
SAMD4A transcript variant X4 XM_047431137.1:c.197-17448= XM_047431137.1:c.197-17449_197-17448insG XM_047431137.1:c.197-17449_197-17448insT
SAMD4A transcript variant X6 XM_047431138.1:c.197-17448= XM_047431138.1:c.197-17449_197-17448insG XM_047431138.1:c.197-17449_197-17448insT
SAMD4A transcript variant X7 XM_047431139.1:c.197-17448= XM_047431139.1:c.197-17449_197-17448insG XM_047431139.1:c.197-17449_197-17448insT
SAMD4A transcript variant X8 XM_047431140.1:c.197-17448= XM_047431140.1:c.197-17449_197-17448insG XM_047431140.1:c.197-17449_197-17448insT
SAMD4A transcript variant X9 XM_047431141.1:c.197-17448= XM_047431141.1:c.197-17449_197-17448insG XM_047431141.1:c.197-17449_197-17448insT
SAMD4A transcript variant X10 XM_047431142.1:c.-108+2557= XM_047431142.1:c.-108+2556_-108+2557insG XM_047431142.1:c.-108+2556_-108+2557insT
SAMD4A transcript variant X11 XM_047431143.1:c.197-17448= XM_047431143.1:c.197-17449_197-17448insG XM_047431143.1:c.197-17449_197-17448insT
SAMD4A transcript variant X12 XM_047431144.1:c.197-17448= XM_047431144.1:c.197-17449_197-17448insG XM_047431144.1:c.197-17449_197-17448insT
SAMD4A transcript variant X13 XM_047431145.1:c.197-17448= XM_047431145.1:c.197-17449_197-17448insG XM_047431145.1:c.197-17449_197-17448insT
SAMD4A transcript variant X14 XM_047431146.1:c.197-17448= XM_047431146.1:c.197-17449_197-17448insG XM_047431146.1:c.197-17449_197-17448insT
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#.

1 SubSNP, 2 Frequency submissions
No Submitter Submission ID Date (Build)
1 GNOMAD ss4278396084 Apr 26, 2021 (155)
2 gnomAD - Genomes NC_000014.9 - 54684614 Apr 26, 2021 (155)
3 ALFA NC_000014.9 - 54684614 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
10635638267 NC_000014.9:54684613::G NC_000014.9:54684613::G (self)
451767192, 10635638267, ss4278396084 NC_000014.9:54684613::T NC_000014.9:54684613::T (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 rs1491469748

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