Skip to main page content
Accesskeys

dbSNP Short Genetic Variations

Reference SNP (rs) Report

Alpha

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.

rs730880252

Current Build 151

Released July 17, 2018

Organism
Homo sapiens
Position
chr6:128883277 (GRCh38.p7) 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
T>C
Variation Type
SNV Single Nucleotide Variation
Frequency
None
Clinical Significance
Reported in ClinVar
Gene : Consequence
LAMA2 : Missense Variant
Publications
1 citation
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.p7 chr 6 NC_000006.12:g.128883277T>C
GRCh37.p13 chr 6 NC_000006.11:g.129204422T>C
LAMA2 RefSeqGene (LRG_409) NG_008678.1:g.5137T>C
Gene: LAMA2, laminin subunit alpha 2 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
LAMA2 transcript variant 1 NM_000426.3:c.32T>C L [CTG] > P [CCG] Coding Sequence Variant
laminin subunit alpha-2 isoform a precursor NP_000417.2:p.Leu...

NP_000417.2:p.Leu11Pro

L (Leu) > P (Pro) Missense Variant
LAMA2 transcript variant 2 NM_001079823.1:c....

NM_001079823.1:c.32T>C

L [CTG] > P [CCG] Coding Sequence Variant
laminin subunit alpha-2 isoform b precursor NP_001073291.1:p....

NP_001073291.1:p.Leu11Pro

L (Leu) > P (Pro) Missense Variant
LAMA2 transcript variant X4 XM_017010851.1:c. N/A Genic Upstream Transcript Variant
LAMA2 transcript variant X5 XM_017010852.1:c. N/A Genic Upstream Transcript Variant
LAMA2 transcript variant X1 XM_005266981.3:c....

XM_005266981.3:c.32T>C

L [CTG] > P [CCG] Coding Sequence Variant
laminin subunit alpha-2 isoform X1 XP_005267038.1:p....

XP_005267038.1:p.Leu11Pro

L (Leu) > P (Pro) Missense Variant
LAMA2 transcript variant X2 XM_011535820.2:c....

XM_011535820.2:c.32T>C

L [CTG] > P [CCG] Coding Sequence Variant
laminin subunit alpha-2 isoform X2 XP_011534122.1:p....

XP_011534122.1:p.Leu11Pro

L (Leu) > P (Pro) Missense Variant
LAMA2 transcript variant X3 XM_005266982.3:c....

XM_005266982.3:c.32T>C

L [CTG] > P [CCG] Coding Sequence Variant
laminin subunit alpha-2 isoform X3 XP_005267039.1:p....

XP_005267039.1:p.Leu11Pro

L (Leu) > P (Pro) Missense Variant
LAMA2 transcript variant X6 XM_017010853.1:c....

XM_017010853.1:c.32T>C

L [CTG] > P [CCG] Coding Sequence Variant
laminin subunit alpha-2 isoform X6 XP_016866342.1:p....

XP_016866342.1:p.Leu11Pro

L (Leu) > P (Pro) Missense 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: C (allele ID: 178769 )
ClinVar Accession Disease Names Clinical Significance
RCV000157587.1 Merosin deficient congenital muscular dystrophy Likely-Pathogenic
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").

None
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 T= C Note
GRCh38.p7 chr 6 NC_000006.12:g.128883277T= NC_000006.12:g.12888327...

NC_000006.12:g.128883277T>C

GRCh37.p13 chr 6 NC_000006.11:g.129204422T= NC_000006.11:g.12920442...

NC_000006.11:g.129204422T>C

LAMA2 RefSeqGene (LRG_409) NG_008678.1:g.5137T= NG_008678.1:g.5137T>C
LAMA2 transcript variant 1 NM_000426.3:c.32T= NM_000426.3:c.32T>C
LAMA2 transcript variant 2 NM_001079823.1:c.32T= NM_001079823.1:c.32T>C
LAMA2 transcript variant X1 XM_005266981.3:c.32T= XM_005266981.3:c.32T>C
LAMA2 transcript variant X1 XM_005266981.1:c.32T= XM_005266981.1:c.32T>C
LAMA2 transcript variant X3 XM_005266982.3:c.32T= XM_005266982.3:c.32T>C
LAMA2 transcript variant X2 XM_005266982.1:c.32T= XM_005266982.1:c.32T>C
LAMA2 transcript variant X2 XM_011535820.2:c.32T= XM_011535820.2:c.32T>C
LAMA2 transcript variant X6 XM_017010853.1:c.32T= XM_017010853.1:c.32T>C
laminin subunit alpha-2 isoform a precursor NP_000417.2:p.Leu11= NP_000417.2:p.Leu11Pro
laminin subunit alpha-2 isoform b precursor NP_001073291.1:p.Leu11= NP_001073291.1:p.Leu11Pro
laminin subunit alpha-2 isoform X1 XP_005267038.1:p.Leu11= XP_005267038.1:p.Leu11Pro
laminin subunit alpha-2 isoform X3 XP_005267039.1:p.Leu11= XP_005267039.1:p.Leu11Pro
laminin subunit alpha-2 isoform X2 XP_011534122.1:p.Leu11= XP_011534122.1:p.Leu11Pro
laminin subunit alpha-2 isoform X6 XP_016866342.1:p.Leu11= XP_016866342.1:p.Leu11Pro
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 ClinVar, 1 SubSNP submissions
No Submitter Submission ID Date (Build)
1 CLINVAR ss1570775644 Feb 26, 2015 (142)
2 ClinVar RCV000157587.1 Jul 20, 2018 (151)
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
ss1570775644 NC_000006.12:128883276:T= NC_000006.12:128883276:T= (self)
RCV000157587.1, ss1570775644 NC_000006.12:128883276:T>C NC_000006.12:128883276:T>C (self)
Help

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

1 citation for rs730880252
PMID Title Author Year Journal
22675738 <i>LAMA2</i>-Related Muscular Dystrophy Quijano-Roy S et al. 1993 GeneReviews®

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: 0.1.4.post833+d3ba21e