chr18-6213175-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_001330559.2(L3MBTL4):c.955G>A(p.Val319Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000463 in 1,599,734 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001330559.2 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
L3MBTL4 | NM_001330559.2 | c.955G>A | p.Val319Ile | missense_variant | 12/19 | ENST00000317931.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
L3MBTL4 | ENST00000317931.12 | c.955G>A | p.Val319Ile | missense_variant | 12/19 | 5 | NM_001330559.2 | P4 | |
L3MBTL4 | ENST00000400104.7 | c.955G>A | p.Val319Ile | missense_variant | 12/17 | 1 | |||
L3MBTL4 | ENST00000400105.6 | c.955G>A | p.Val319Ile | missense_variant | 12/20 | 2 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.000263 AC: 40AN: 152156Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000742 AC: 18AN: 242566Hom.: 0 AF XY: 0.0000918 AC XY: 12AN XY: 130760
GnomAD4 exome AF: 0.0000235 AC: 34AN: 1447578Hom.: 0 Cov.: 28 AF XY: 0.0000292 AC XY: 21AN XY: 719950
GnomAD4 genome ? AF: 0.000263 AC: 40AN: 152156Hom.: 0 Cov.: 33 AF XY: 0.000229 AC XY: 17AN XY: 74338
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 01, 2024 | 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