rs11967042
Positions:
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_000426.4(LAMA2):c.3037+49G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.103 in 1,504,734 control chromosomes in the GnomAD database, including 11,065 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.12 ( 1433 hom., cov: 33)
Exomes 𝑓: 0.10 ( 9632 hom. )
Consequence
LAMA2
NM_000426.4 intron
NM_000426.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.36
Genes affected
LAMA2 (HGNC:6482): (laminin subunit alpha 2) Laminin, an extracellular protein, is a major component of the basement membrane. It is thought to mediate the attachment, migration, and organization of cells into tissues during embryonic development by interacting with other extracellular matrix components. It is composed of three subunits, alpha, beta, and gamma, which are bound to each other by disulfide bonds into a cross-shaped molecule. This gene encodes the alpha 2 chain, which constitutes one of the subunits of laminin 2 (merosin) and laminin 4 (s-merosin). Mutations in this gene have been identified as the cause of congenital merosin-deficient muscular dystrophy. Two transcript variants encoding different proteins have been found for this gene. [provided by RefSeq, Jul 2008]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BP6
?
Variant 6-129297914-G-A is Benign according to our data. Variant chr6-129297914-G-A is described in ClinVar as [Benign]. Clinvar id is 256063.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr6-129297914-G-A is described in Lovd as [Benign].
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.386 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LAMA2 | NM_000426.4 | c.3037+49G>A | intron_variant | ENST00000421865.3 | |||
LAMA2 | NM_001079823.2 | c.3037+49G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LAMA2 | ENST00000421865.3 | c.3037+49G>A | intron_variant | 5 | NM_000426.4 | ||||
LAMA2 | ENST00000617695.5 | c.3037+49G>A | intron_variant | 5 | |||||
LAMA2 | ENST00000618192.5 | c.3301+49G>A | intron_variant | 5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.117 AC: 17728AN: 151976Hom.: 1430 Cov.: 33
GnomAD3 genomes
?
AF:
AC:
17728
AN:
151976
Hom.:
Cov.:
33
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.143 AC: 30729AN: 214394Hom.: 3194 AF XY: 0.135 AC XY: 15562AN XY: 114978
GnomAD3 exomes
AF:
AC:
30729
AN:
214394
Hom.:
AF XY:
AC XY:
15562
AN XY:
114978
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.102 AC: 137753AN: 1352640Hom.: 9632 Cov.: 20 AF XY: 0.101 AC XY: 68130AN XY: 676048
GnomAD4 exome
AF:
AC:
137753
AN:
1352640
Hom.:
Cov.:
20
AF XY:
AC XY:
68130
AN XY:
676048
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.117 AC: 17749AN: 152094Hom.: 1433 Cov.: 33 AF XY: 0.123 AC XY: 9121AN XY: 74350
GnomAD4 genome
?
AF:
AC:
17749
AN:
152094
Hom.:
Cov.:
33
AF XY:
AC XY:
9121
AN XY:
74350
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
706
AN:
3478
ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 18, 2018 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at