rs149254699
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 0P and 3B. BP4_ModerateBP7
The NM_000426.4(LAMA2):c.2766C>A(p.Ala922=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000682 in 1,613,686 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. A922A) has been classified as Likely benign.
Frequency
Consequence
NM_000426.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LAMA2 | NM_000426.4 | c.2766C>A | p.Ala922= | synonymous_variant | 20/65 | ENST00000421865.3 | |
LAMA2 | NM_001079823.2 | c.2766C>A | p.Ala922= | synonymous_variant | 20/64 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LAMA2 | ENST00000421865.3 | c.2766C>A | p.Ala922= | synonymous_variant | 20/65 | 5 | NM_000426.4 | ||
LAMA2 | ENST00000618192.5 | c.2766C>A | p.Ala922= | synonymous_variant | 20/66 | 5 | P1 | ||
LAMA2 | ENST00000617695.5 | c.2766C>A | p.Ala922= | synonymous_variant | 20/64 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152170Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 251412Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135878
GnomAD4 exome AF: 0.00000616 AC: 9AN: 1461516Hom.: 0 Cov.: 30 AF XY: 0.00000413 AC XY: 3AN XY: 727098
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152170Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74342
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at