11-72089135-T-C
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_145309.6(LRRC51):āc.52T>Cā(p.Tyr18His) variant causes a missense change. The variant allele was found at a frequency of 0.000105 in 1,614,008 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Consequence
NM_145309.6 missense
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 |
---|---|---|---|---|---|---|---|---|
LRRC51 | NM_145309.6 | c.52T>C | p.Tyr18His | missense_variant | Exon 3 of 6 | ENST00000289488.8 | NP_660352.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000723 AC: 11AN: 152134Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000593 AC: 149AN: 251476Hom.: 1 AF XY: 0.000324 AC XY: 44AN XY: 135914
GnomAD4 exome AF: 0.000108 AC: 158AN: 1461874Hom.: 1 Cov.: 31 AF XY: 0.0000646 AC XY: 47AN XY: 727238
GnomAD4 genome AF: 0.0000723 AC: 11AN: 152134Hom.: 0 Cov.: 32 AF XY: 0.0000807 AC XY: 6AN XY: 74336
ClinVar
Submissions by phenotype
not provided Benign:1
- -
LRTOMT-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at