chr19-5893087-A-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_001193375.3(NDUFA11):c.517T>A(p.Cys173Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000128 in 1,536,062 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001193375.3 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 |
---|---|---|---|---|---|---|---|
NDUFA11 | NM_001193375.3 | c.517T>A | p.Cys173Ser | missense_variant | 4/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NDUFA11 | ENST00000418389.6 | c.517T>A | p.Cys173Ser | missense_variant | 4/4 | 2 |
Frequencies
GnomAD3 genomes AF: 0.000519 AC: 79AN: 152112Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000197 AC: 27AN: 136750Hom.: 0 AF XY: 0.000202 AC XY: 15AN XY: 74340
GnomAD4 exome AF: 0.0000838 AC: 116AN: 1383832Hom.: 0 Cov.: 32 AF XY: 0.0000879 AC XY: 60AN XY: 682864
GnomAD4 genome AF: 0.000526 AC: 80AN: 152230Hom.: 0 Cov.: 32 AF XY: 0.000470 AC XY: 35AN XY: 74434
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 03, 2015 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at