NM_198129.4:c.160C>T
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_198129.4(LAMA3):c.160C>T(p.Leu54Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000901 in 1,553,776 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
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LAMA3 | ENST00000313654.14 | c.160C>T | p.Leu54Leu | synonymous_variant | Exon 1 of 75 | 1 | NM_198129.4 | ENSP00000324532.8 | ||
LAMA3 | ENST00000399516.7 | c.160C>T | p.Leu54Leu | synonymous_variant | Exon 1 of 74 | 1 | ENSP00000382432.2 | |||
LAMA3 | ENST00000585600.5 | n.160C>T | non_coding_transcript_exon_variant | Exon 1 of 13 | 1 | ENSP00000468316.1 |
Frequencies
GnomAD3 genomes AF: 0.000585 AC: 89AN: 152244Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000742 AC: 11AN: 148322Hom.: 0 AF XY: 0.0000741 AC XY: 6AN XY: 80982
GnomAD4 exome AF: 0.0000364 AC: 51AN: 1401418Hom.: 0 Cov.: 31 AF XY: 0.0000275 AC XY: 19AN XY: 691972
GnomAD4 genome AF: 0.000584 AC: 89AN: 152358Hom.: 0 Cov.: 32 AF XY: 0.000671 AC XY: 50AN XY: 74504
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