11-62671975-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The ENST00000377953.4(UQCC3):c.143G>A(p.Arg48Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00011 in 1,614,020 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R48G) has been classified as Uncertain significance.
Frequency
Consequence
ENST00000377953.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
UQCC3 | NM_001085372.3 | c.143G>A | p.Arg48Lys | missense_variant | 2/2 | ENST00000377953.4 | NP_001078841.1 | |
LBHD1 | NM_024099.5 | c.-422C>T | 5_prime_UTR_variant | 1/7 | ENST00000354588.8 | NP_077004.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
UQCC3 | ENST00000377953.4 | c.143G>A | p.Arg48Lys | missense_variant | 2/2 | 1 | NM_001085372.3 | ENSP00000367189 | P1 | |
LBHD1 | ENST00000354588.8 | c.-422C>T | 5_prime_UTR_variant | 1/7 | 1 | NM_024099.5 | ENSP00000346600 | P1 | ||
UQCC3 | ENST00000531323.1 | c.143G>A | p.Arg48Lys | missense_variant | 3/3 | 3 | ENSP00000432692 | P1 | ||
LBHD1 | ENST00000528862.2 | c.93+152C>T | intron_variant | 3 | ENSP00000434489 |
Frequencies
GnomAD3 genomes AF: 0.000315 AC: 48AN: 152256Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000404 AC: 10AN: 247396Hom.: 0 AF XY: 0.0000371 AC XY: 5AN XY: 134648
GnomAD4 exome AF: 0.0000883 AC: 129AN: 1461646Hom.: 0 Cov.: 31 AF XY: 0.0000756 AC XY: 55AN XY: 727118
GnomAD4 genome AF: 0.000315 AC: 48AN: 152374Hom.: 0 Cov.: 32 AF XY: 0.000362 AC XY: 27AN XY: 74522
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Oct 02, 2022 | In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated. This variant has not been reported in the literature in individuals affected with UQCC3-related conditions. This variant is present in population databases (rs199794771, gnomAD 0.01%). This sequence change replaces arginine, which is basic and polar, with lysine, which is basic and polar, at codon 48 of the UQCC3 protein (p.Arg48Lys). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at