rs121912517
Variant summary
Our verdict is Likely pathogenic. Variant got 8 ACMG points: 8P and 0B. PM2PM5PP3_Strong
The NM_000894.3(LHB):āc.167G>Cā(p.Gly56Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000686 in 1,457,552 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G56D) has been classified as Pathogenic.
Frequency
Consequence
NM_000894.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LHB | NM_000894.3 | c.167G>C | p.Gly56Ala | missense_variant | 2/3 | ENST00000649238.3 | |
LHB | XM_047438832.1 | c.215G>C | p.Gly72Ala | missense_variant | 1/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LHB | ENST00000649238.3 | c.167G>C | p.Gly56Ala | missense_variant | 2/3 | NM_000894.3 | P1 | ||
LHB | ENST00000649284.1 | n.258G>C | non_coding_transcript_exon_variant | 1/2 |
Frequencies
GnomAD3 genomes ? Cov.: 29
GnomAD3 exomes AF: 0.00000402 AC: 1AN: 248728Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 134900
GnomAD4 exome AF: 6.86e-7 AC: 1AN: 1457552Hom.: 0 Cov.: 84 AF XY: 0.00 AC XY: 0AN XY: 725258
GnomAD4 genome ? Cov.: 29
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at