rs200095274
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 2P and 12B. PM5BP4_StrongBP6_Very_Strong
The NM_000426.4(LAMA2):āc.7772A>Gā(p.Asn2591Ser) variant causes a missense change. The variant allele was found at a frequency of 0.0000781 in 1,613,678 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. N2591?) has been classified as Likely pathogenic.
Frequency
Consequence
NM_000426.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LAMA2 | NM_000426.4 | c.7772A>G | p.Asn2591Ser | missense_variant | 56/65 | ENST00000421865.3 | |
LAMA2 | NM_001079823.2 | c.7760A>G | p.Asn2587Ser | missense_variant | 55/64 | ||
LOC124901401 | XR_007059767.1 | upstream_gene_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LAMA2 | ENST00000421865.3 | c.7772A>G | p.Asn2591Ser | missense_variant | 56/65 | 5 | NM_000426.4 | ||
ENST00000665046.1 | n.975+16109T>C | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.0000657 AC: 10AN: 152166Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000187 AC: 47AN: 250978Hom.: 0 AF XY: 0.000192 AC XY: 26AN XY: 135630
GnomAD4 exome AF: 0.0000794 AC: 116AN: 1461512Hom.: 0 Cov.: 43 AF XY: 0.0000894 AC XY: 65AN XY: 727082
GnomAD4 genome ? AF: 0.0000657 AC: 10AN: 152166Hom.: 0 Cov.: 32 AF XY: 0.0000673 AC XY: 5AN XY: 74324
ClinVar
Submissions by phenotype
LAMA2-related muscular dystrophy Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 04, 2024 | - - |
LAMA2-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jan 14, 2020 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at