6-129369966-C-T
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7
The NM_000426.4(LAMA2):c.4935C>T(p.Thr1645Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000136 in 1,613,772 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 (★). Synonymous variant affecting the same amino acid position (i.e. T1645T) has been classified as Likely benign.
Frequency
Consequence
NM_000426.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LAMA2 | ENST00000421865.3 | c.4935C>T | p.Thr1645Thr | synonymous_variant | Exon 34 of 65 | 5 | NM_000426.4 | ENSP00000400365.2 | ||
LAMA2 | ENST00000618192.5 | c.5199C>T | p.Thr1733Thr | synonymous_variant | Exon 35 of 66 | 5 | ENSP00000480802.2 | |||
LAMA2 | ENST00000617695.5 | c.4935C>T | p.Thr1645Thr | synonymous_variant | Exon 34 of 64 | 5 | ENSP00000481744.2 | |||
LAMA2 | ENST00000687590.1 | n.1355C>T | non_coding_transcript_exon_variant | Exon 2 of 5 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152028Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000279 AC: 7AN: 250750Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135496
GnomAD4 exome AF: 0.0000123 AC: 18AN: 1461744Hom.: 0 Cov.: 31 AF XY: 0.00000963 AC XY: 7AN XY: 727172
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152028Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74234
ClinVar
Submissions by phenotype
LAMA2-related muscular dystrophy Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at