6-112120322-A-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.4626T>C(p.Ile1542Ile) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000558 in 1,614,022 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_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.4626T>C | p.Ile1542Ile | synonymous_variant | Exon 33 of 39 | ENST00000230538.12 | NP_001098676.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LAMA4 | ENST00000230538.12 | c.4626T>C | p.Ile1542Ile | synonymous_variant | Exon 33 of 39 | 1 | NM_001105206.3 | ENSP00000230538.7 |
Frequencies
GnomAD3 genomes AF: 0.000283 AC: 43AN: 152200Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000837 AC: 21AN: 250908Hom.: 0 AF XY: 0.0000737 AC XY: 10AN XY: 135602
GnomAD4 exome AF: 0.0000322 AC: 47AN: 1461704Hom.: 0 Cov.: 32 AF XY: 0.0000261 AC XY: 19AN XY: 727150
GnomAD4 genome AF: 0.000282 AC: 43AN: 152318Hom.: 0 Cov.: 33 AF XY: 0.000282 AC XY: 21AN XY: 74478
ClinVar
Submissions by phenotype
not specified Benign:1
p.Ile1535Ile in Exon 33 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. It has been identified in 0.1% (3/3738) of Af rican American chromosomes from a broad population by the NHLBI Exome Sequencing Project (http://evs.gs.washington.edu/EVS; dbSNP rs150791451). -
Dilated cardiomyopathy 1JJ Benign:1
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not provided Benign:1
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Cardiovascular phenotype Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at