rs121912539
Variant summary
Our verdict is Uncertain significance. Variant got 5 ACMG points: 5P and 0B. PM2PP3_ModeratePP5
The NM_000233.4(LHCGR):c.430G>T(p.Val144Phe) variant causes a missense change. The variant allele was found at a frequency of 0.00000479 in 1,461,614 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V144I) has been classified as Likely benign.
Frequency
Consequence
NM_000233.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LHCGR | NM_000233.4 | c.430G>T | p.Val144Phe | missense_variant | 5/11 | ENST00000294954.12 | |
STON1-GTF2A1L | NM_001198593.2 | c.3441+51970C>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LHCGR | ENST00000294954.12 | c.430G>T | p.Val144Phe | missense_variant | 5/11 | 1 | NM_000233.4 | A2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251144Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135728
GnomAD4 exome AF: 0.00000479 AC: 7AN: 1461614Hom.: 0 Cov.: 30 AF XY: 0.00000688 AC XY: 5AN XY: 727128
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Leydig cell agenesis Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Oct 01, 2004 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at