rs786205414
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 1P and 4B. PM4_SupportingBS2
The NM_001105208.3(LAMA4):c.266_268delTCT(p.Phe89del) variant causes a disruptive inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000657 in 1,614,174 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★★).
Frequency
Consequence
NM_001105208.3 disruptive_inframe_deletion
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LAMA4 | NM_001105206.3 | c.195+71_195+73delTCT | intron_variant | Intron 2 of 38 | ENST00000230538.12 | NP_001098676.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LAMA4 | ENST00000230538.12 | c.195+71_195+73delTCT | intron_variant | Intron 2 of 38 | 1 | NM_001105206.3 | ENSP00000230538.7 | |||
ENSG00000281613 | ENST00000587816.2 | c.-398+16969_-398+16971delAAG | intron_variant | Intron 1 of 4 | 5 | ENSP00000487146.1 |
Frequencies
GnomAD3 genomes AF: 0.000387 AC: 59AN: 152266Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000432 AC: 108AN: 250150Hom.: 0 AF XY: 0.000413 AC XY: 56AN XY: 135600
GnomAD4 exome AF: 0.000685 AC: 1001AN: 1461790Hom.: 0 AF XY: 0.000659 AC XY: 479AN XY: 727194
GnomAD4 genome AF: 0.000387 AC: 59AN: 152384Hom.: 0 Cov.: 32 AF XY: 0.000309 AC XY: 23AN XY: 74516
ClinVar
Submissions by phenotype
Dilated cardiomyopathy 1JJ Uncertain:1
LAMA4 NM_001105208.2 exon 2 p.Phe89del (c.266_268del): This variant has not been reported in the literature and is present in 0.06% (81/128678) of European alleles in the Genome Aggregation Database (http://gnomad.broadinstitute.org/variant/6-112575084-GAGA-G). This variant is present in ClinVar (Variation ID:191693). Evolutionary conservation and computational predictive tools for this variant are limited or unavailable. This variant represents an in-frame deletion of one amino acid at position 89 and is not predicted to alter the reading frame. However, the effect of this variant on the protein is unclear. In summary, data on this variant is insufficient for disease classification. Therefore, the clinical significance of this variant is uncertain. -
not provided Uncertain:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at