chr6-129252238-A-G
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4_StrongBP6
The NM_000426.4(LAMA2):āc.2039A>Gā(p.Asn680Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000403 in 1,614,016 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_000426.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LAMA2 | NM_000426.4 | c.2039A>G | p.Asn680Ser | missense_variant | 14/65 | ENST00000421865.3 | |
LAMA2 | NM_001079823.2 | c.2039A>G | p.Asn680Ser | missense_variant | 14/64 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LAMA2 | ENST00000421865.3 | c.2039A>G | p.Asn680Ser | missense_variant | 14/65 | 5 | NM_000426.4 | ||
LAMA2 | ENST00000618192.5 | c.2039A>G | p.Asn680Ser | missense_variant | 14/66 | 5 | P1 | ||
LAMA2 | ENST00000617695.5 | c.2039A>G | p.Asn680Ser | missense_variant | 14/64 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152204Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000676 AC: 17AN: 251302Hom.: 0 AF XY: 0.0000663 AC XY: 9AN XY: 135812
GnomAD4 exome AF: 0.0000424 AC: 62AN: 1461812Hom.: 0 Cov.: 31 AF XY: 0.0000413 AC XY: 30AN XY: 727208
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152204Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74362
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 05, 2022 | The c.2039A>G (p.N680S) alteration is located in exon 14 (coding exon 14) of the LAMA2 gene. This alteration results from a A to G substitution at nucleotide position 2039, causing the asparagine (N) at amino acid position 680 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
LAMA2-related muscular dystrophy Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 03, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at