12-56471554-A-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_013267.4(GLS2):c.1742T>A(p.Leu581His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,461,800 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign 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. L581F) has been classified as Uncertain significance.
Frequency
Consequence
NM_013267.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GLS2 | NM_013267.4 | c.1742T>A | p.Leu581His | missense_variant | 18/18 | ENST00000311966.9 | |
SPRYD4 | NM_207344.4 | c.*1977A>T | 3_prime_UTR_variant | 2/2 | ENST00000338146.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GLS2 | ENST00000311966.9 | c.1742T>A | p.Leu581His | missense_variant | 18/18 | 1 | NM_013267.4 | P1 | |
SPRYD4 | ENST00000338146.7 | c.*1977A>T | 3_prime_UTR_variant | 2/2 | 1 | NM_207344.4 | P1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461800Hom.: 0 Cov.: 33 AF XY: 0.00000138 AC XY: 1AN XY: 727198
GnomAD4 genome Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at