19-19516266-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PP3_ModerateBS2
The NM_015965.7(NDUFA13):āc.28A>Gā(p.Met10Val) variant causes a missense change. The variant allele was found at a frequency of 0.0000198 in 1,613,826 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_015965.7 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NDUFA13 | ENST00000507754.9 | c.28A>G | p.Met10Val | missense_variant | Exon 1 of 5 | 1 | NM_015965.7 | ENSP00000423673.1 | ||
ENSG00000258674 | ENST00000555938.1 | c.28A>G | p.Met10Val | missense_variant | Exon 1 of 7 | 2 | ENSP00000452549.1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152186Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000798 AC: 2AN: 250748Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135818
GnomAD4 exome AF: 0.0000205 AC: 30AN: 1461640Hom.: 0 Cov.: 32 AF XY: 0.0000220 AC XY: 16AN XY: 727124
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152186Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74342
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
The c.28A>G (p.M10V) alteration is located in exon 1 (coding exon 1) of the NDUFA13 gene. This alteration results from a A to G substitution at nucleotide position 28, causing the methionine (M) at amino acid position 10 to be replaced by a valine (V). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at