6-112122175-T-G
Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_001105206.3(LAMA4):c.4314A>C(p.Ser1438Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000464 in 1,613,812 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_001105206.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -17 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LAMA4 | NM_001105206.3 | c.4314A>C | p.Ser1438Ser | synonymous_variant | Exon 32 of 39 | ENST00000230538.12 | NP_001098676.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LAMA4 | ENST00000230538.12 | c.4314A>C | p.Ser1438Ser | synonymous_variant | Exon 32 of 39 | 1 | NM_001105206.3 | ENSP00000230538.7 |
Frequencies
GnomAD3 genomes AF: 0.00232 AC: 353AN: 152170Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000597 AC: 150AN: 251064Hom.: 0 AF XY: 0.000442 AC XY: 60AN XY: 135672
GnomAD4 exome AF: 0.000266 AC: 389AN: 1461524Hom.: 2 Cov.: 32 AF XY: 0.000224 AC XY: 163AN XY: 727090
GnomAD4 genome AF: 0.00236 AC: 360AN: 152288Hom.: 2 Cov.: 32 AF XY: 0.00227 AC XY: 169AN XY: 74486
ClinVar
Submissions by phenotype
not specified Benign:3
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
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p.Ser1431Ser in Exon 32 of LAMA4: This variant is not expected to have clinical significance because it does not alter an amino acid residue, is not located wit hin the splice consensus sequence and has been identified in 0.9% (33/3738) of A frican American chromosomes from a broad population by the NHLBI Exome Sequencin g Project (http://evs.gs.washington.edu/EVS; dbSNP rs77367833). -
Dilated cardiomyopathy 1JJ Benign:3
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not provided Benign:1
LAMA4: BS1, BS2 -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at