11-62671942-C-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_024099.5(LBHD1):c.-389G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00181 in 1,613,812 control chromosomes in the GnomAD database, including 56 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_024099.5 5_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LBHD1 | NM_024099.5 | c.-389G>A | 5_prime_UTR_variant | Exon 1 of 7 | ENST00000354588.8 | NP_077004.2 | ||
UQCC3 | NM_001085372.3 | c.121-11C>T | 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.-389G>A | 5_prime_UTR_variant | Exon 1 of 7 | 1 | NM_024099.5 | ENSP00000346600.3 | |||
UQCC3 | ENST00000377953.4 | c.121-11C>T | intron_variant | Intron 1 of 1 | 1 | NM_001085372.3 | ENSP00000367189.3 | |||
LBHD1 | ENST00000528862.2 | c.93+185G>A | intron_variant | Intron 1 of 2 | 3 | ENSP00000434489.2 | ||||
UQCC3 | ENST00000531323.1 | c.121-11C>T | intron_variant | Intron 2 of 2 | 3 | ENSP00000432692.1 |
Frequencies
GnomAD3 genomes AF: 0.00986 AC: 1501AN: 152212Hom.: 27 Cov.: 32
GnomAD3 exomes AF: 0.00235 AC: 582AN: 247738Hom.: 6 AF XY: 0.00173 AC XY: 233AN XY: 134760
GnomAD4 exome AF: 0.000961 AC: 1404AN: 1461482Hom.: 29 Cov.: 31 AF XY: 0.000792 AC XY: 576AN XY: 727022
GnomAD4 genome AF: 0.00991 AC: 1509AN: 152330Hom.: 27 Cov.: 32 AF XY: 0.00960 AC XY: 715AN XY: 74494
ClinVar
Submissions by phenotype
not provided Benign:2
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not specified 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