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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.

rs1483732800

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr18:23894984 (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
C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.000004 (1/250300, GnomAD_exome)
T=0.0001 (1/8988, ALFA)
Clinical Significance
Reported in ClinVar
Gene : Consequence
LAMA3 : Synonymous 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 8988 C=0.9999 T=0.0001 0.999777 0.0 0.000223 0
European Sub 6062 C=0.9998 T=0.0002 0.99967 0.0 0.00033 0
African Sub 594 C=1.000 T=0.000 1.0 0.0 0.0 N/A
African Others Sub 8 C=1.0 T=0.0 1.0 0.0 0.0 N/A
African American Sub 586 C=1.000 T=0.000 1.0 0.0 0.0 N/A
Asian Sub 56 C=1.00 T=0.00 1.0 0.0 0.0 N/A
East Asian Sub 26 C=1.00 T=0.00 1.0 0.0 0.0 N/A
Other Asian Sub 30 C=1.00 T=0.00 1.0 0.0 0.0 N/A
Latin American 1 Sub 0 C=0 T=0 0 0 0 N/A
Latin American 2 Sub 0 C=0 T=0 0 0 0 N/A
South Asian Sub 0 C=0 T=0 0 0 0 N/A
Other Sub 2276 C=1.0000 T=0.0000 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 - Exomes Global Study-wide 250300 C=0.999996 T=0.000004
gnomAD - Exomes European Sub 134626 C=1.000000 T=0.000000
gnomAD - Exomes Asian Sub 48828 C=1.00000 T=0.00000
gnomAD - Exomes American Sub 34492 C=1.00000 T=0.00000
gnomAD - Exomes African Sub 16168 C=1.00000 T=0.00000
gnomAD - Exomes Ashkenazi Jewish Sub 10070 C=1.00000 T=0.00000
gnomAD - Exomes Other Sub 6116 C=0.9998 T=0.0002
Allele Frequency Aggregator Total Global 8988 C=0.9999 T=0.0001
Allele Frequency Aggregator European Sub 6062 C=0.9998 T=0.0002
Allele Frequency Aggregator Other Sub 2276 C=1.0000 T=0.0000
Allele Frequency Aggregator African Sub 594 C=1.000 T=0.000
Allele Frequency Aggregator Asian Sub 56 C=1.00 T=0.00
Allele Frequency Aggregator Latin American 1 Sub 0 C=0 T=0
Allele Frequency Aggregator Latin American 2 Sub 0 C=0 T=0
Allele Frequency Aggregator South Asian Sub 0 C=0 T=0
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.23894984C>T
GRCh37.p13 chr 18 NC_000018.9:g.21474948C>T
LAMA3 RefSeqGene NG_007853.2:g.210387C>T
Gene: LAMA3, laminin subunit alpha 3 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
LAMA3 transcript variant 5 NM_001302996.2:c. N/A Genic Downstream Transcript Variant
LAMA3 transcript variant 1 NM_198129.4:c.5539C>T L [CTG] > L [TTG] Coding Sequence Variant
laminin subunit alpha-3 isoform 1 precursor NP_937762.2:p.Leu1847= L (Leu) > L (Leu) Synonymous Variant
LAMA3 transcript variant 3 NM_001127717.4:c.5539C>T L [CTG] > L [TTG] Coding Sequence Variant
laminin subunit alpha-3 isoform 3 precursor NP_001121189.2:p.Leu1847= L (Leu) > L (Leu) Synonymous Variant
LAMA3 transcript variant 4 NM_001127718.4:c.712C>T L [CTG] > L [TTG] Coding Sequence Variant
laminin subunit alpha-3 isoform 4 precursor NP_001121190.2:p.Leu238= L (Leu) > L (Leu) Synonymous Variant
LAMA3 transcript variant 2 NM_000227.6:c.712C>T L [CTG] > L [TTG] Coding Sequence Variant
laminin subunit alpha-3 isoform 2 precursor NP_000218.3:p.Leu238= L (Leu) > L (Leu) Synonymous Variant
LAMA3 transcript variant 6 NR_130106.2:n. N/A Genic Downstream Transcript Variant
LAMA3 transcript variant X10 XM_017025743.1:c.3418C>T L [CTG] > L [TTG] Coding Sequence Variant
laminin subunit alpha-3 isoform X10 XP_016881232.1:p.Leu1140= L (Leu) > L (Leu) Synonymous Variant
LAMA3 transcript variant X1 XM_011525978.3:c.5566C>T L [CTG] > L [TTG] Coding Sequence Variant
laminin subunit alpha-3 isoform X1 XP_011524280.1:p.Leu1856= L (Leu) > L (Leu) Synonymous Variant
LAMA3 transcript variant X2 XM_011525979.3:c.5557C>T L [CTG] > L [TTG] Coding Sequence Variant
laminin subunit alpha-3 isoform X2 XP_011524281.1:p.Leu1853= L (Leu) > L (Leu) Synonymous Variant
LAMA3 transcript variant X3 XM_011525980.3:c.5548C>T L [CTG] > L [TTG] Coding Sequence Variant
laminin subunit alpha-3 isoform X3 XP_011524282.1:p.Leu1850= L (Leu) > L (Leu) Synonymous Variant
LAMA3 transcript variant X4 XM_011525981.3:c.5434C>T L [CTG] > L [TTG] Coding Sequence Variant
laminin subunit alpha-3 isoform X4 XP_011524283.1:p.Leu1812= L (Leu) > L (Leu) Synonymous Variant
LAMA3 transcript variant X5 XM_047437503.1:c.5425C>T L [CTG] > L [TTG] Coding Sequence Variant
laminin subunit alpha-3 isoform X5 XP_047293459.1:p.Leu1809= L (Leu) > L (Leu) Synonymous Variant
LAMA3 transcript variant X6 XM_047437504.1:c.5407C>T L [CTG] > L [TTG] Coding Sequence Variant
laminin subunit alpha-3 isoform X6 XP_047293460.1:p.Leu1803= L (Leu) > L (Leu) Synonymous Variant
LAMA3 transcript variant X7 XM_047437505.1:c.5566C>T L [CTG] > L [TTG] Coding Sequence Variant
laminin subunit alpha-3 isoform X7 XP_047293461.1:p.Leu1856= L (Leu) > L (Leu) Synonymous Variant
LAMA3 transcript variant X8 XM_011525982.3:c.5566C>T L [CTG] > L [TTG] Coding Sequence Variant
laminin subunit alpha-3 isoform X8 XP_011524284.1:p.Leu1856= L (Leu) > L (Leu) Synonymous Variant
LAMA3 transcript variant X9 XM_047437506.1:c.5539C>T L [CTG] > L [TTG] Coding Sequence Variant
laminin subunit alpha-3 isoform X9 XP_047293462.1:p.Leu1847= L (Leu) > L (Leu) Synonymous Variant
LAMA3 transcript variant X11 XM_017025744.2:c.1108C>T L [CTG] > L [TTG] Coding Sequence Variant
laminin subunit alpha-3 isoform X11 XP_016881233.1:p.Leu370= L (Leu) > L (Leu) Synonymous 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.

Allele: T (allele ID: 1083933 )
ClinVar Accession Disease Names Clinical Significance
RCV001402475.4 not provided Likely-Benign
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 C= T
GRCh38.p14 chr 18 NC_000018.10:g.23894984= NC_000018.10:g.23894984C>T
GRCh37.p13 chr 18 NC_000018.9:g.21474948= NC_000018.9:g.21474948C>T
LAMA3 RefSeqGene NG_007853.2:g.210387= NG_007853.2:g.210387C>T
LAMA3 transcript variant 2 NM_000227.6:c.712= NM_000227.6:c.712C>T
LAMA3 transcript variant 2 NM_000227.5:c.712= NM_000227.5:c.712C>T
LAMA3 transcript variant 2 NM_000227.4:c.712= NM_000227.4:c.712C>T
LAMA3 transcript variant 2 NM_000227.3:c.712= NM_000227.3:c.712C>T
LAMA3 transcript variant 1 NM_198129.4:c.5539= NM_198129.4:c.5539C>T
LAMA3 transcript variant 1 NM_198129.3:c.5539= NM_198129.3:c.5539C>T
LAMA3 transcript variant 1 NM_198129.2:c.5539= NM_198129.2:c.5539C>T
LAMA3 transcript variant 1 NM_198129.1:c.5539= NM_198129.1:c.5539C>T
LAMA3 transcript variant 3 NM_001127717.4:c.5539= NM_001127717.4:c.5539C>T
LAMA3 transcript variant 3 NM_001127717.3:c.5539= NM_001127717.3:c.5539C>T
LAMA3 transcript variant 3 NM_001127717.2:c.5539= NM_001127717.2:c.5539C>T
LAMA3 transcript variant 3 NM_001127717.1:c.5539= NM_001127717.1:c.5539C>T
LAMA3 transcript variant 4 NM_001127718.4:c.712= NM_001127718.4:c.712C>T
LAMA3 transcript variant 4 NM_001127718.3:c.712= NM_001127718.3:c.712C>T
LAMA3 transcript variant 4 NM_001127718.2:c.712= NM_001127718.2:c.712C>T
LAMA3 transcript variant 4 NM_001127718.1:c.712= NM_001127718.1:c.712C>T
LAMA3 transcript variant X1 XM_011525978.3:c.5566= XM_011525978.3:c.5566C>T
LAMA3 transcript variant X1 XM_011525978.2:c.5566= XM_011525978.2:c.5566C>T
LAMA3 transcript variant X1 XM_011525978.1:c.5566= XM_011525978.1:c.5566C>T
LAMA3 transcript variant X2 XM_011525979.3:c.5557= XM_011525979.3:c.5557C>T
LAMA3 transcript variant X2 XM_011525979.2:c.5557= XM_011525979.2:c.5557C>T
LAMA3 transcript variant X2 XM_011525979.1:c.5557= XM_011525979.1:c.5557C>T
LAMA3 transcript variant X3 XM_011525980.3:c.5548= XM_011525980.3:c.5548C>T
LAMA3 transcript variant X3 XM_011525980.2:c.5548= XM_011525980.2:c.5548C>T
LAMA3 transcript variant X3 XM_011525980.1:c.5548= XM_011525980.1:c.5548C>T
LAMA3 transcript variant X4 XM_011525981.3:c.5434= XM_011525981.3:c.5434C>T
LAMA3 transcript variant X4 XM_011525981.2:c.5434= XM_011525981.2:c.5434C>T
LAMA3 transcript variant X4 XM_011525981.1:c.5434= XM_011525981.1:c.5434C>T
LAMA3 transcript variant X8 XM_011525982.3:c.5566= XM_011525982.3:c.5566C>T
LAMA3 transcript variant X6 XM_011525982.2:c.5566= XM_011525982.2:c.5566C>T
LAMA3 transcript variant X5 XM_011525982.1:c.5566= XM_011525982.1:c.5566C>T
LAMA3 transcript variant X11 XM_017025744.2:c.1108= XM_017025744.2:c.1108C>T
LAMA3 transcript variant X8 XM_017025744.1:c.1108= XM_017025744.1:c.1108C>T
LAMA3 transcript variant X5 XM_047437503.1:c.5425= XM_047437503.1:c.5425C>T
LAMA3 transcript variant X6 XM_047437504.1:c.5407= XM_047437504.1:c.5407C>T
LAMA3 transcript variant X9 XM_047437506.1:c.5539= XM_047437506.1:c.5539C>T
LAMA3 transcript variant X7 XM_047437505.1:c.5566= XM_047437505.1:c.5566C>T
LAMA3 transcript variant X10 XM_017025743.1:c.3418= XM_017025743.1:c.3418C>T
laminin subunit alpha-3 isoform 2 precursor NP_000218.3:p.Leu238= NP_000218.3:p.Leu238=
laminin subunit alpha-3 isoform 1 precursor NP_937762.2:p.Leu1847= NP_937762.2:p.Leu1847=
laminin subunit alpha-3 isoform 3 precursor NP_001121189.2:p.Leu1847= NP_001121189.2:p.Leu1847=
laminin subunit alpha-3 isoform 4 precursor NP_001121190.2:p.Leu238= NP_001121190.2:p.Leu238=
laminin subunit alpha-3 isoform X1 XP_011524280.1:p.Leu1856= XP_011524280.1:p.Leu1856=
laminin subunit alpha-3 isoform X2 XP_011524281.1:p.Leu1853= XP_011524281.1:p.Leu1853=
laminin subunit alpha-3 isoform X3 XP_011524282.1:p.Leu1850= XP_011524282.1:p.Leu1850=
laminin subunit alpha-3 isoform X4 XP_011524283.1:p.Leu1812= XP_011524283.1:p.Leu1812=
laminin subunit alpha-3 isoform X8 XP_011524284.1:p.Leu1856= XP_011524284.1:p.Leu1856=
laminin subunit alpha-3 isoform X11 XP_016881233.1:p.Leu370= XP_016881233.1:p.Leu370=
laminin subunit alpha-3 isoform X5 XP_047293459.1:p.Leu1809= XP_047293459.1:p.Leu1809=
laminin subunit alpha-3 isoform X6 XP_047293460.1:p.Leu1803= XP_047293460.1:p.Leu1803=
laminin subunit alpha-3 isoform X9 XP_047293462.1:p.Leu1847= XP_047293462.1:p.Leu1847=
laminin subunit alpha-3 isoform X7 XP_047293461.1:p.Leu1856= XP_047293461.1:p.Leu1856=
laminin subunit alpha-3 isoform X10 XP_016881232.1:p.Leu1140= XP_016881232.1:p.Leu1140=
laminin subunit alpha-3 isoform 2 precursor NP_000218.2:p.Leu238= NP_000218.2:p.Leu238=
laminin subunit alpha-3 isoform 3 precursor NP_001121189.1:p.Leu1847= NP_001121189.1:p.Leu1847=
laminin subunit alpha-3 isoform 4 precursor NP_001121190.1:p.Leu238= NP_001121190.1:p.Leu238=
laminin subunit alpha-3 isoform 1 precursor NP_937762.1:p.Leu1847= NP_937762.1:p.Leu1847=
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, 2 Frequency, 1 ClinVar submissions
No Submitter Submission ID Date (Build)
1 GNOMAD ss2743228764 Nov 08, 2017 (151)
2 EVA ss5430347104 Oct 16, 2022 (156)
3 gnomAD - Exomes NC_000018.9 - 21474948 Jul 13, 2019 (153)
4 ALFA NC_000018.10 - 23894984 Apr 27, 2021 (155)
5 ClinVar RCV001402475.4 Oct 16, 2022 (156)
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
12539223, ss2743228764, ss5430347104 NC_000018.9:21474947:C:T NC_000018.10:23894983:C:T (self)
RCV001402475.4, 8600799173 NC_000018.10:23894983:C:T NC_000018.10:23894983:C: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 rs1483732800

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