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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.

rs1491503854

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr9:89457242-89457243 (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
delAG
Variation Type
Deletion
Frequency
delAG=0.00000 (0/11862, ALFA)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
SEMA4D : 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 AG=1.00000 =0.00000 1.0 0.0 0.0 N/A
European Sub 7618 AG=1.0000 =0.0000 1.0 0.0 0.0 N/A
African Sub 2816 AG=1.0000 =0.0000 1.0 0.0 0.0 N/A
African Others Sub 108 AG=1.000 =0.000 1.0 0.0 0.0 N/A
African American Sub 2708 AG=1.0000 =0.0000 1.0 0.0 0.0 N/A
Asian Sub 108 AG=1.000 =0.000 1.0 0.0 0.0 N/A
East Asian Sub 84 AG=1.00 =0.00 1.0 0.0 0.0 N/A
Other Asian Sub 24 AG=1.00 =0.00 1.0 0.0 0.0 N/A
Latin American 1 Sub 146 AG=1.000 =0.000 1.0 0.0 0.0 N/A
Latin American 2 Sub 610 AG=1.000 =0.000 1.0 0.0 0.0 N/A
South Asian Sub 94 AG=1.00 =0.00 1.0 0.0 0.0 N/A
Other Sub 470 AG=1.000 =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
Allele Frequency Aggregator Total Global 11862 AG=1.00000 delAG=0.00000
Allele Frequency Aggregator European Sub 7618 AG=1.0000 delAG=0.0000
Allele Frequency Aggregator African Sub 2816 AG=1.0000 delAG=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 AG=1.000 delAG=0.000
Allele Frequency Aggregator Other Sub 470 AG=1.000 delAG=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 AG=1.000 delAG=0.000
Allele Frequency Aggregator Asian Sub 108 AG=1.000 delAG=0.000
Allele Frequency Aggregator South Asian Sub 94 AG=1.00 delAG=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 9 NC_000009.12:g.89457242_89457243del
GRCh37.p13 chr 9 NC_000009.11:g.92072157_92072158del
Gene: SEMA4D, semaphorin 4D (minus strand)
Molecule type Change Amino acid[Codon] SO Term
SEMA4D transcript variant 2 NM_001142287.2:c.-447-129…

NM_001142287.2:c.-447-1290_-447-1289del

N/A Intron Variant
SEMA4D transcript variant 3 NM_001371194.2:c.-309-129…

NM_001371194.2:c.-309-1290_-309-1289del

N/A Intron Variant
SEMA4D transcript variant 4 NM_001371195.1:c.-372-129…

NM_001371195.1:c.-372-1290_-372-1289del

N/A Intron Variant
SEMA4D transcript variant 5 NM_001371196.1:c.-447-129…

NM_001371196.1:c.-447-1290_-447-1289del

N/A Intron Variant
SEMA4D transcript variant 6 NM_001371197.1:c.-372-129…

NM_001371197.1:c.-372-1290_-372-1289del

N/A Intron Variant
SEMA4D transcript variant 7 NM_001371198.1:c.-309-129…

NM_001371198.1:c.-309-1290_-309-1289del

N/A Intron Variant
SEMA4D transcript variant 8 NM_001371199.1:c.-372-129…

NM_001371199.1:c.-372-1290_-372-1289del

N/A Intron Variant
SEMA4D transcript variant 9 NM_001371200.1:c.-447-129…

NM_001371200.1:c.-447-1290_-447-1289del

N/A Intron Variant
SEMA4D transcript variant 10 NM_001371201.1:c.-309-129…

NM_001371201.1:c.-309-1290_-309-1289del

N/A Intron Variant
SEMA4D transcript variant 11 NM_001371202.1:c.-372-129…

NM_001371202.1:c.-372-1290_-372-1289del

N/A Intron Variant
SEMA4D transcript variant 1 NM_006378.4:c.-447-1290_-…

NM_006378.4:c.-447-1290_-447-1289del

N/A Intron Variant
SEMA4D transcript variant 12 NR_163884.1:n. N/A Intron Variant
SEMA4D transcript variant 13 NR_163885.1:n. N/A Intron Variant
SEMA4D transcript variant 14 NR_163886.1:n. N/A Intron Variant
SEMA4D transcript variant 15 NR_163887.1:n. N/A Intron Variant
SEMA4D transcript variant 16 NR_163888.1:n. N/A Intron Variant
SEMA4D transcript variant 17 NR_163889.1:n. N/A Intron Variant
SEMA4D transcript variant X4 XM_011518123.3:c.-447-129…

XM_011518123.3:c.-447-1290_-447-1289del

N/A Intron Variant
SEMA4D transcript variant X8 XM_011518124.3:c.-447-129…

XM_011518124.3:c.-447-1290_-447-1289del

N/A Intron Variant
SEMA4D transcript variant X9 XM_011518125.2:c.-447-129…

XM_011518125.2:c.-447-1290_-447-1289del

N/A Intron Variant
SEMA4D transcript variant X6 XM_011518127.3:c.-447-129…

XM_011518127.3:c.-447-1290_-447-1289del

N/A Intron Variant
SEMA4D transcript variant X14 XM_011518128.3:c.-372-129…

XM_011518128.3:c.-372-1290_-372-1289del

N/A Intron Variant
SEMA4D transcript variant X22 XM_011518129.2:c.-372-129…

XM_011518129.2:c.-372-1290_-372-1289del

N/A Intron Variant
SEMA4D transcript variant X3 XM_011518133.3:c.-309-129…

XM_011518133.3:c.-309-1290_-309-1289del

N/A Intron Variant
SEMA4D transcript variant X7 XM_017014193.3:c.-447-129…

XM_017014193.3:c.-447-1290_-447-1289del

N/A Intron Variant
SEMA4D transcript variant X13 XM_017014194.2:c.-372-129…

XM_017014194.2:c.-372-1290_-372-1289del

N/A Intron Variant
SEMA4D transcript variant X21 XM_017014195.2:c.-309-129…

XM_017014195.2:c.-309-1290_-309-1289del

N/A Intron Variant
SEMA4D transcript variant X19 XM_017014198.2:c.-309-129…

XM_017014198.2:c.-309-1290_-309-1289del

N/A Intron Variant
SEMA4D transcript variant X1 XM_047422606.1:c.-372-129…

XM_047422606.1:c.-372-1290_-372-1289del

N/A Intron Variant
SEMA4D transcript variant X2 XM_047422607.1:c.-372-129…

XM_047422607.1:c.-372-1290_-372-1289del

N/A Intron Variant
SEMA4D transcript variant X10 XM_047422609.1:c.-447-129…

XM_047422609.1:c.-447-1290_-447-1289del

N/A Intron Variant
SEMA4D transcript variant X12 XM_047422614.1:c.-309-129…

XM_047422614.1:c.-309-1290_-309-1289del

N/A Intron Variant
SEMA4D transcript variant X15 XM_047422617.1:c.-372-129…

XM_047422617.1:c.-372-1290_-372-1289del

N/A Intron Variant
SEMA4D transcript variant X23 XM_047422619.1:c.-309-129…

XM_047422619.1:c.-309-1290_-309-1289del

N/A Intron Variant
SEMA4D transcript variant X24 XM_047422620.1:c.-447-129…

XM_047422620.1:c.-447-1290_-447-1289del

N/A Intron Variant
SEMA4D transcript variant X27 XM_047422623.1:c.-309-129…

XM_047422623.1:c.-309-1290_-309-1289del

N/A Intron Variant
SEMA4D transcript variant X28 XM_047422624.1:c.-309-129…

XM_047422624.1:c.-309-1290_-309-1289del

N/A Intron Variant
SEMA4D transcript variant X31 XM_047422627.1:c.-309-129…

XM_047422627.1:c.-309-1290_-309-1289del

N/A Intron Variant
SEMA4D transcript variant X33 XM_047422629.1:c.-447-129…

XM_047422629.1:c.-447-1290_-447-1289del

N/A Intron Variant
SEMA4D transcript variant X34 XM_047422630.1:c.-447-129…

XM_047422630.1:c.-447-1290_-447-1289del

N/A Intron Variant
SEMA4D transcript variant X37 XM_047422631.1:c.-372-129…

XM_047422631.1:c.-372-1290_-372-1289del

N/A Intron Variant
SEMA4D transcript variant X36 XM_047422632.1:c.-309-129…

XM_047422632.1:c.-309-1290_-309-1289del

N/A Intron Variant
SEMA4D transcript variant X38 XM_047422634.1:c.-309-129…

XM_047422634.1:c.-309-1290_-309-1289del

N/A Intron Variant
SEMA4D transcript variant X11 XM_011518130.3:c. N/A Genic Upstream Transcript Variant
SEMA4D transcript variant X16 XM_011518131.3:c. N/A Genic Upstream Transcript Variant
SEMA4D transcript variant X5 XM_011518134.3:c. N/A Genic Upstream Transcript Variant
SEMA4D transcript variant X39 XM_047422610.1:c. N/A Genic Upstream Transcript Variant
SEMA4D transcript variant X17 XM_047422611.1:c. N/A Genic Upstream Transcript Variant
SEMA4D transcript variant X40 XM_047422612.1:c. N/A Genic Upstream Transcript Variant
SEMA4D transcript variant X41 XM_047422613.1:c. N/A Genic Upstream Transcript Variant
SEMA4D transcript variant X20 XM_047422615.1:c. N/A Genic Upstream Transcript Variant
SEMA4D transcript variant X18 XM_047422618.1:c. N/A Genic Upstream Transcript Variant
SEMA4D transcript variant X25 XM_047422621.1:c. N/A Genic Upstream Transcript Variant
SEMA4D transcript variant X26 XM_047422622.1:c. N/A Genic Upstream Transcript Variant
SEMA4D transcript variant X29 XM_047422625.1:c. N/A Genic Upstream Transcript Variant
SEMA4D transcript variant X30 XM_047422626.1:c. N/A Genic Upstream Transcript Variant
SEMA4D transcript variant X32 XM_047422628.1:c. N/A Genic Upstream Transcript Variant
SEMA4D transcript variant X35 XM_047422633.1:c. 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 AG= delAG
GRCh38.p14 chr 9 NC_000009.12:g.89457242_89457243= NC_000009.12:g.89457242_89457243del
GRCh37.p13 chr 9 NC_000009.11:g.92072157_92072158= NC_000009.11:g.92072157_92072158del
SEMA4D transcript variant 2 NM_001142287.1:c.-447-1289= NM_001142287.1:c.-447-1290_-447-1289del
SEMA4D transcript variant 2 NM_001142287.2:c.-447-1289= NM_001142287.2:c.-447-1290_-447-1289del
SEMA4D transcript variant 3 NM_001371194.2:c.-309-1289= NM_001371194.2:c.-309-1290_-309-1289del
SEMA4D transcript variant 4 NM_001371195.1:c.-372-1289= NM_001371195.1:c.-372-1290_-372-1289del
SEMA4D transcript variant 5 NM_001371196.1:c.-447-1289= NM_001371196.1:c.-447-1290_-447-1289del
SEMA4D transcript variant 6 NM_001371197.1:c.-372-1289= NM_001371197.1:c.-372-1290_-372-1289del
SEMA4D transcript variant 7 NM_001371198.1:c.-309-1289= NM_001371198.1:c.-309-1290_-309-1289del
SEMA4D transcript variant 8 NM_001371199.1:c.-372-1289= NM_001371199.1:c.-372-1290_-372-1289del
SEMA4D transcript variant 9 NM_001371200.1:c.-447-1289= NM_001371200.1:c.-447-1290_-447-1289del
SEMA4D transcript variant 10 NM_001371201.1:c.-309-1289= NM_001371201.1:c.-309-1290_-309-1289del
SEMA4D transcript variant 11 NM_001371202.1:c.-372-1289= NM_001371202.1:c.-372-1290_-372-1289del
SEMA4D transcript variant 1 NM_006378.3:c.-447-1289= NM_006378.3:c.-447-1290_-447-1289del
SEMA4D transcript variant 1 NM_006378.4:c.-447-1289= NM_006378.4:c.-447-1290_-447-1289del
SEMA4D transcript variant X1 XM_005251647.1:c.-372-1289= XM_005251647.1:c.-372-1290_-372-1289del
SEMA4D transcript variant X2 XM_005251648.1:c.-372-1289= XM_005251648.1:c.-372-1290_-372-1289del
SEMA4D transcript variant X3 XM_005251649.1:c.-372-1289= XM_005251649.1:c.-372-1290_-372-1289del
SEMA4D transcript variant X4 XM_005251650.1:c.-372-1289= XM_005251650.1:c.-372-1290_-372-1289del
SEMA4D transcript variant X5 XM_005251651.1:c.-447-1289= XM_005251651.1:c.-447-1290_-447-1289del
SEMA4D transcript variant X7 XM_005251653.1:c.-309-1289= XM_005251653.1:c.-309-1290_-309-1289del
SEMA4D transcript variant X8 XM_005251654.1:c.-309-1289= XM_005251654.1:c.-309-1290_-309-1289del
SEMA4D transcript variant X4 XM_011518123.3:c.-447-1289= XM_011518123.3:c.-447-1290_-447-1289del
SEMA4D transcript variant X8 XM_011518124.3:c.-447-1289= XM_011518124.3:c.-447-1290_-447-1289del
SEMA4D transcript variant X9 XM_011518125.2:c.-447-1289= XM_011518125.2:c.-447-1290_-447-1289del
SEMA4D transcript variant X6 XM_011518127.3:c.-447-1289= XM_011518127.3:c.-447-1290_-447-1289del
SEMA4D transcript variant X14 XM_011518128.3:c.-372-1289= XM_011518128.3:c.-372-1290_-372-1289del
SEMA4D transcript variant X22 XM_011518129.2:c.-372-1289= XM_011518129.2:c.-372-1290_-372-1289del
SEMA4D transcript variant X3 XM_011518133.3:c.-309-1289= XM_011518133.3:c.-309-1290_-309-1289del
SEMA4D transcript variant X7 XM_017014193.3:c.-447-1289= XM_017014193.3:c.-447-1290_-447-1289del
SEMA4D transcript variant X13 XM_017014194.2:c.-372-1289= XM_017014194.2:c.-372-1290_-372-1289del
SEMA4D transcript variant X21 XM_017014195.2:c.-309-1289= XM_017014195.2:c.-309-1290_-309-1289del
SEMA4D transcript variant X19 XM_017014198.2:c.-309-1289= XM_017014198.2:c.-309-1290_-309-1289del
SEMA4D transcript variant X1 XM_047422606.1:c.-372-1289= XM_047422606.1:c.-372-1290_-372-1289del
SEMA4D transcript variant X2 XM_047422607.1:c.-372-1289= XM_047422607.1:c.-372-1290_-372-1289del
SEMA4D transcript variant X10 XM_047422609.1:c.-447-1289= XM_047422609.1:c.-447-1290_-447-1289del
SEMA4D transcript variant X12 XM_047422614.1:c.-309-1289= XM_047422614.1:c.-309-1290_-309-1289del
SEMA4D transcript variant X15 XM_047422617.1:c.-372-1289= XM_047422617.1:c.-372-1290_-372-1289del
SEMA4D transcript variant X23 XM_047422619.1:c.-309-1289= XM_047422619.1:c.-309-1290_-309-1289del
SEMA4D transcript variant X24 XM_047422620.1:c.-447-1289= XM_047422620.1:c.-447-1290_-447-1289del
SEMA4D transcript variant X27 XM_047422623.1:c.-309-1289= XM_047422623.1:c.-309-1290_-309-1289del
SEMA4D transcript variant X28 XM_047422624.1:c.-309-1289= XM_047422624.1:c.-309-1290_-309-1289del
SEMA4D transcript variant X31 XM_047422627.1:c.-309-1289= XM_047422627.1:c.-309-1290_-309-1289del
SEMA4D transcript variant X33 XM_047422629.1:c.-447-1289= XM_047422629.1:c.-447-1290_-447-1289del
SEMA4D transcript variant X34 XM_047422630.1:c.-447-1289= XM_047422630.1:c.-447-1290_-447-1289del
SEMA4D transcript variant X37 XM_047422631.1:c.-372-1289= XM_047422631.1:c.-372-1290_-372-1289del
SEMA4D transcript variant X36 XM_047422632.1:c.-309-1289= XM_047422632.1:c.-309-1290_-309-1289del
SEMA4D transcript variant X38 XM_047422634.1:c.-309-1289= XM_047422634.1:c.-309-1290_-309-1289del
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, 1 Frequency submissions
No Submitter Submission ID Date (Build)
1 EVA_DECODE ss3724275708 Jul 13, 2019 (153)
2 ALFA NC_000009.12 - 89457242 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
1092714844, ss3724275708 NC_000009.12:89457241:AG: NC_000009.12:89457241:AG: (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 rs1491503854

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