chr12-101766274-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_024312.5(GNPTAB):āc.1429T>Cā(p.Tyr477His) variant causes a missense change. The variant allele was found at a frequency of 0.0000112 in 1,613,550 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts 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. Y477D) has been classified as Likely benign.
Frequency
Consequence
NM_024312.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GNPTAB | NM_024312.5 | c.1429T>C | p.Tyr477His | missense_variant | 12/21 | ENST00000299314.12 | |
GNPTAB | XM_011538731.3 | c.1348T>C | p.Tyr450His | missense_variant | 12/21 | ||
GNPTAB | XM_006719593.4 | c.1429T>C | p.Tyr477His | missense_variant | 12/19 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GNPTAB | ENST00000299314.12 | c.1429T>C | p.Tyr477His | missense_variant | 12/21 | 1 | NM_024312.5 | P1 | |
GNPTAB | ENST00000552009.1 | n.88T>C | non_coding_transcript_exon_variant | 2/2 | 3 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152142Hom.: 0 Cov.: 33
GnomAD4 exome AF: 0.0000116 AC: 17AN: 1461408Hom.: 0 Cov.: 30 AF XY: 0.0000124 AC XY: 9AN XY: 727028
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152142Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74314
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at