rs863224081
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Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBS1BS2
The NM_004544.4(NDUFA10):c.1000-10del variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000791 in 1,573,550 control chromosomes in the GnomAD database, including 18 homozygotes. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.00049 ( 1 hom., cov: 33)
Exomes 𝑓: 0.00082 ( 17 hom. )
Consequence
NDUFA10
NM_004544.4 splice_polypyrimidine_tract, intron
NM_004544.4 splice_polypyrimidine_tract, intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -0.305
Genes affected
NDUFA10 (HGNC:7684): (NADH:ubiquinone oxidoreductase subunit A10) The protein encoded by this gene is a component of 42 kDa complex I, the first enzyme complex in the electron transport chain of mitochondria. This protein has NADH dehydrogenase activity and oxidoreductase activity. It transfers electrons from NADH to the respiratory chain. A mutation in this gene was found in an individual with Leigh syndrome. [provided by RefSeq, Apr 2016]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -16 ACMG points.
BP6
?
Variant 2-239961195-GA-G is Benign according to our data. Variant chr2-239961195-GA-G is described in ClinVar as [Likely_benign]. Clinvar id is 214700.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS1
?
Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.000493 (73/148118) while in subpopulation SAS AF= 0.00745 (35/4700). AF 95% confidence interval is 0.0055. There are 1 homozygotes in gnomad4. There are 47 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAdExome4 at 17 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NDUFA10 | NM_004544.4 | c.1000-10del | splice_polypyrimidine_tract_variant, intron_variant | ENST00000252711.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NDUFA10 | ENST00000252711.7 | c.1000-10del | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_004544.4 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.000493 AC: 73AN: 148004Hom.: 1 Cov.: 33
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GnomAD3 exomes AF: 0.00146 AC: 365AN: 250656Hom.: 4 AF XY: 0.00202 AC XY: 274AN XY: 135556
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GnomAD4 exome AF: 0.000822 AC: 1171AN: 1425432Hom.: 17 Cov.: 34 AF XY: 0.00119 AC XY: 847AN XY: 709548
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GnomAD4 genome ? AF: 0.000493 AC: 73AN: 148118Hom.: 1 Cov.: 33 AF XY: 0.000652 AC XY: 47AN XY: 72082
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:4
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:3
Likely benign, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Mar 30, 2017 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Mar 12, 2023 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Oct 26, 2017 | 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. - |
not specified Benign:1
Benign, flagged submission | clinical testing | GeneDx | Apr 02, 2014 | The variant is found in MITONUC-MITOP panel(s). - |
Computational scores
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at