19-19516268-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 1P and 5B. PP3BS1_SupportingBS2
The NM_015965.7(NDUFA13):c.30G>A(p.Met10Ile) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000149 in 1,613,844 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 (★).
Frequency
Consequence
NM_015965.7 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NDUFA13 | ENST00000507754.9 | c.30G>A | p.Met10Ile | missense_variant | Exon 1 of 5 | 1 | NM_015965.7 | ENSP00000423673.1 | ||
ENSG00000258674 | ENST00000555938.1 | c.30G>A | p.Met10Ile | missense_variant | Exon 1 of 7 | 2 | ENSP00000452549.1 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152210Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000678 AC: 17AN: 250630Hom.: 0 AF XY: 0.0000589 AC XY: 8AN XY: 135794
GnomAD4 exome AF: 0.0000144 AC: 21AN: 1461634Hom.: 0 Cov.: 32 AF XY: 0.0000179 AC XY: 13AN XY: 727124
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152210Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74356
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
The c.30G>A (p.M10I) alteration is located in exon 1 (coding exon 1) of the NDUFA13 gene. This alteration results from a G to A substitution at nucleotide position 30, causing the methionine (M) at amino acid position 10 to be replaced by an isoleucine (I). 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