5-1325759-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_030782.5(CLPTM1L):c.1138G>A(p.Glu380Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00066 in 1,613,284 control chromosomes in the GnomAD database, including 4 homozygotes. 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 Benign (★).
Frequency
Consequence
NM_030782.5 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CLPTM1L | NM_030782.5 | c.1138G>A | p.Glu380Lys | missense_variant | 10/17 | ENST00000320895.10 | |
CLPTM1L | XM_011514144.3 | c.1135G>A | p.Glu379Lys | missense_variant | 10/17 | ||
CLPTM1L | XM_024446222.2 | c.604G>A | p.Glu202Lys | missense_variant | 8/15 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CLPTM1L | ENST00000320895.10 | c.1138G>A | p.Glu380Lys | missense_variant | 10/17 | 1 | NM_030782.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000808 AC: 123AN: 152196Hom.: 1 Cov.: 33
GnomAD3 exomes AF: 0.000911 AC: 229AN: 251344Hom.: 0 AF XY: 0.000913 AC XY: 124AN XY: 135852
GnomAD4 exome AF: 0.000645 AC: 942AN: 1460970Hom.: 3 Cov.: 30 AF XY: 0.000644 AC XY: 468AN XY: 726816
GnomAD4 genome ? AF: 0.000808 AC: 123AN: 152314Hom.: 1 Cov.: 33 AF XY: 0.000819 AC XY: 61AN XY: 74482
ClinVar
Submissions by phenotype
CLPTM1L-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Aug 15, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at