chr6-129481390-G-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_000426.4(LAMA2):āc.7700G>Cā(p.Ser2567Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,461,698 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S2567N) has been classified as Uncertain significance.
Frequency
Consequence
NM_000426.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LAMA2 | NM_000426.4 | c.7700G>C | p.Ser2567Thr | missense_variant | 55/65 | ENST00000421865.3 | |
LOC124901401 | XR_007059767.1 | n.4993C>G | non_coding_transcript_exon_variant | 2/2 | |||
LAMA2 | NM_001079823.2 | c.7688G>C | p.Ser2563Thr | missense_variant | 54/64 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LAMA2 | ENST00000421865.3 | c.7700G>C | p.Ser2567Thr | missense_variant | 55/65 | 5 | NM_000426.4 | ||
ENST00000442449.1 | n.21C>G | non_coding_transcript_exon_variant | 1/2 | 5 | |||||
ENST00000665046.1 | n.975+21215C>G | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461698Hom.: 0 Cov.: 32 AF XY: 0.00000275 AC XY: 2AN XY: 727154
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Merosin deficient congenital muscular dystrophy Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Center For Human Genetics And Laboratory Diagnostics, Dr. Klein, Dr. Rost And Colleagues | Feb 22, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at