18-23689803-G-A
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_198129.4(LAMA3):c.120G>A(p.Gly40Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000644 in 1,537,132 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_198129.4 synonymous
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LAMA3 | ENST00000313654.14 | c.120G>A | p.Gly40Gly | synonymous_variant | Exon 1 of 75 | 1 | NM_198129.4 | ENSP00000324532.8 | ||
LAMA3 | ENST00000399516.7 | c.120G>A | p.Gly40Gly | synonymous_variant | Exon 1 of 74 | 1 | ENSP00000382432.2 | |||
LAMA3 | ENST00000585600.5 | n.120G>A | non_coding_transcript_exon_variant | Exon 1 of 13 | 1 | ENSP00000468316.1 |
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152200Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000162 AC: 21AN: 129356Hom.: 0 AF XY: 0.000155 AC XY: 11AN XY: 71050
GnomAD4 exome AF: 0.0000657 AC: 91AN: 1384932Hom.: 0 Cov.: 31 AF XY: 0.0000630 AC XY: 43AN XY: 683050
GnomAD4 genome AF: 0.0000526 AC: 8AN: 152200Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74360
ClinVar
Submissions by phenotype
not provided Benign:1
- -
LAMA3-related disorder Benign:1
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