21-42893344-C-G
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_021075.4(NDUFV3):āc.11C>Gā(p.Pro4Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0018 in 1,538,452 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_021075.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NDUFV3 | NM_021075.4 | c.11C>G | p.Pro4Arg | missense_variant | 1/4 | ENST00000354250.7 | NP_066553.3 | |
NDUFV3 | NM_001001503.2 | c.11C>G | p.Pro4Arg | missense_variant | 1/3 | NP_001001503.1 | ||
NDUFV3 | XM_011529586.3 | c.11C>G | p.Pro4Arg | missense_variant | 1/5 | XP_011527888.1 | ||
NDUFV3 | XM_017028359.2 | c.11C>G | p.Pro4Arg | missense_variant | 1/4 | XP_016883848.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NDUFV3 | ENST00000354250.7 | c.11C>G | p.Pro4Arg | missense_variant | 1/4 | 1 | NM_021075.4 | ENSP00000346196 | ||
NDUFV3 | ENST00000340344.4 | c.11C>G | p.Pro4Arg | missense_variant | 1/3 | 1 | ENSP00000342895 | P1 | ||
NDUFV3 | ENST00000460740.1 | n.24C>G | non_coding_transcript_exon_variant | 1/2 | 2 | |||||
NDUFV3 | ENST00000460259.1 | n.572-3583C>G | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.00140 AC: 213AN: 152242Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00167 AC: 224AN: 134158Hom.: 0 AF XY: 0.00197 AC XY: 144AN XY: 73120
GnomAD4 exome AF: 0.00184 AC: 2557AN: 1386092Hom.: 2 Cov.: 31 AF XY: 0.00193 AC XY: 1321AN XY: 684066
GnomAD4 genome AF: 0.00140 AC: 213AN: 152360Hom.: 0 Cov.: 32 AF XY: 0.00142 AC XY: 106AN XY: 74510
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Dec 31, 2019 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | Nov 14, 2023 | - - |
NDUFV3-related disorder Benign:1
Likely benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 03, 2022 | 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). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at