11-72293408-G-A
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001258392.3(CLPB):c.1993C>T(p.Arg665Trp) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000562 in 1,614,144 control chromosomes in the GnomAD database, including 6 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001258392.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CLPB | NM_030813.6 | c.2083C>T | p.Arg695Trp | missense_variant | Exon 17 of 17 | ENST00000294053.9 | NP_110440.1 | |
CLPB | NM_001258392.3 | c.1993C>T | p.Arg665Trp | missense_variant | Exon 16 of 16 | ENST00000538039.6 | NP_001245321.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CLPB | ENST00000294053.9 | c.2083C>T | p.Arg695Trp | missense_variant | Exon 17 of 17 | 1 | NM_030813.6 | ENSP00000294053.3 | ||
CLPB | ENST00000538039.6 | c.1993C>T | p.Arg665Trp | missense_variant | Exon 16 of 16 | 2 | NM_001258392.3 | ENSP00000441518.1 |
Frequencies
GnomAD3 genomes AF: 0.00302 AC: 460AN: 152164Hom.: 5 Cov.: 32
GnomAD3 exomes AF: 0.000736 AC: 185AN: 251380Hom.: 1 AF XY: 0.000537 AC XY: 73AN XY: 135872
GnomAD4 exome AF: 0.000306 AC: 447AN: 1461862Hom.: 1 Cov.: 31 AF XY: 0.000261 AC XY: 190AN XY: 727224
GnomAD4 genome AF: 0.00302 AC: 460AN: 152282Hom.: 5 Cov.: 32 AF XY: 0.00314 AC XY: 234AN XY: 74458
ClinVar
Submissions by phenotype
not provided Benign:3
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
CLPB: BP4, BS1, BS2 -
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CLPB-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
3-methylglutaconic aciduria, type VIIB Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at