chr8-97775937-C-CGGCGGGCTCCAGGCGAGGCGGGCTCCAGGCGA
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The ENST00000445593.6(LAPTM4B):c.222_223insGCTCCAGGCGAGGCGGGCTCCAGGCGAGGCGG(p.Ser75AlafsTer15) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000107 in 1,451,714 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
ENST00000445593.6 frameshift
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LAPTM4B | ENST00000445593.6 | c.222_223insGCTCCAGGCGAGGCGGGCTCCAGGCGAGGCGG | p.Ser75AlafsTer15 | frameshift_variant | Exon 1 of 7 | 1 | ENSP00000402301.2 | |||
LAPTM4B | ENST00000619747.1 | c.222_223insGCTCCAGGCGAGGCGGGCTCCAGGCGAGGCGG | p.Ser75AlafsTer15 | frameshift_variant | Exon 1 of 7 | 1 | ENSP00000482533.1 | |||
LAPTM4B | ENST00000521545 | c.-52_-51insGCTCCAGGCGAGGCGGGCTCCAGGCGAGGCGG | 5_prime_UTR_variant | Exon 1 of 7 | 1 | NM_018407.6 | ENSP00000428409.1 | |||
LAPTM4B | ENST00000517924 | c.-52_-51insGCTCCAGGCGAGGCGGGCTCCAGGCGAGGCGG | 5_prime_UTR_variant | Exon 1 of 5 | 5 | ENSP00000429868.2 |
Frequencies
GnomAD3 genomes AF: 0.000152 AC: 23AN: 151808Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000316 AC: 2AN: 63330Hom.: 0 AF XY: 0.0000547 AC XY: 2AN XY: 36534
GnomAD4 exome AF: 0.000102 AC: 133AN: 1299796Hom.: 0 Cov.: 35 AF XY: 0.000106 AC XY: 68AN XY: 638880
GnomAD4 genome AF: 0.000151 AC: 23AN: 151918Hom.: 0 Cov.: 31 AF XY: 0.000121 AC XY: 9AN XY: 74258
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at