11-62671832-C-T
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_001085372.3(UQCC3):c.87C>T(p.Thr29Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000514 in 1,614,136 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001085372.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
UQCC3 | NM_001085372.3 | c.87C>T | p.Thr29Thr | synonymous_variant | Exon 1 of 2 | ENST00000377953.4 | NP_001078841.1 | |
LBHD1 | NM_024099.5 | c.-279G>A | 5_prime_UTR_variant | Exon 1 of 7 | ENST00000354588.8 | NP_077004.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
UQCC3 | ENST00000377953.4 | c.87C>T | p.Thr29Thr | synonymous_variant | Exon 1 of 2 | 1 | NM_001085372.3 | ENSP00000367189.3 | ||
LBHD1 | ENST00000354588.8 | c.-279G>A | 5_prime_UTR_variant | Exon 1 of 7 | 1 | NM_024099.5 | ENSP00000346600.3 | |||
UQCC3 | ENST00000531323.1 | c.87C>T | p.Thr29Thr | synonymous_variant | Exon 2 of 3 | 3 | ENSP00000432692.1 | |||
LBHD1 | ENST00000528862.2 | c.93+295G>A | intron_variant | Intron 1 of 2 | 3 | ENSP00000434489.2 |
Frequencies
GnomAD3 genomes AF: 0.0000657 AC: 10AN: 152174Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000128 AC: 32AN: 249124Hom.: 0 AF XY: 0.000126 AC XY: 17AN XY: 135296
GnomAD4 exome AF: 0.0000499 AC: 73AN: 1461844Hom.: 0 Cov.: 31 AF XY: 0.0000468 AC XY: 34AN XY: 727232
GnomAD4 genome AF: 0.0000657 AC: 10AN: 152292Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74454
ClinVar
Submissions by phenotype
not provided Benign:1
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. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at