11-62671945-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_001085372.3(UQCC3):c.121-8G>A variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000428 in 1,613,786 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001085372.3 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LBHD1 | NM_024099.5 | c.-392C>T | 5_prime_UTR_variant | Exon 1 of 7 | ENST00000354588.8 | NP_077004.2 | ||
UQCC3 | NM_001085372.3 | c.121-8G>A | splice_region_variant, intron_variant | Intron 1 of 1 | ENST00000377953.4 | NP_001078841.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LBHD1 | ENST00000354588.8 | c.-392C>T | 5_prime_UTR_variant | Exon 1 of 7 | 1 | NM_024099.5 | ENSP00000346600.3 | |||
UQCC3 | ENST00000377953.4 | c.121-8G>A | splice_region_variant, intron_variant | Intron 1 of 1 | 1 | NM_001085372.3 | ENSP00000367189.3 | |||
LBHD1 | ENST00000528862.2 | c.93+182C>T | intron_variant | Intron 1 of 2 | 3 | ENSP00000434489.2 | ||||
UQCC3 | ENST00000531323.1 | c.121-8G>A | splice_region_variant, intron_variant | Intron 2 of 2 | 3 | ENSP00000432692.1 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152212Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000121 AC: 3AN: 247584Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 134686
GnomAD4 exome AF: 0.0000452 AC: 66AN: 1461574Hom.: 1 Cov.: 31 AF XY: 0.0000426 AC XY: 31AN XY: 727086
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152212Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74374
ClinVar
Submissions by phenotype
not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at