chr19-29213103-A-C
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_006003.3(UQCRFS1):c.16T>G(p.Ser6Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.928 in 152,110 control chromosomes in the GnomAD database, including 65,583 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another nucleotide change resulting in the same amino acid substitution has been previously reported as Likely benign in UniProt.
Frequency
Consequence
NM_006003.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
UQCRFS1 | ENST00000304863.6 | c.16T>G | p.Ser6Ala | missense_variant | Exon 1 of 2 | 1 | NM_006003.3 | ENSP00000306397.3 | ||
UQCRFS1-DT | ENST00000587859.1 | n.-132A>C | upstream_gene_variant | 2 | ||||||
UQCRFS1-DT | ENST00000590607.2 | n.-180A>C | upstream_gene_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.928 AC: 141118AN: 151998Hom.: 65530 Cov.: 36
GnomAD3 exomes AF: 0.932 AC: 101723AN: 109136Hom.: 47498 AF XY: 0.932 AC XY: 56697AN XY: 60804
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.923 AC: 1256870AN: 1362224Hom.: 580235 Cov.: 50 AF XY: 0.923 AC XY: 620649AN XY: 672332
GnomAD4 genome AF: 0.928 AC: 141226AN: 152110Hom.: 65583 Cov.: 36 AF XY: 0.930 AC XY: 69156AN XY: 74346
ClinVar
Submissions by phenotype
not provided Benign:1
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Mitochondrial complex 3 deficiency, nuclear type 10 Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at