rs1063739
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_005309.3(GPT):c.40C>A(p.His14Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.466 in 1,610,178 control chromosomes in the GnomAD database, including 178,460 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 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 nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. H14D) has been classified as Benign.
Frequency
Consequence
NM_005309.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GPT | NM_005309.3 | c.40C>A | p.His14Asn | missense_variant | 1/11 | ENST00000394955.3 | |
LOC101928953 | XR_007061149.1 | n.103+1028G>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GPT | ENST00000394955.3 | c.40C>A | p.His14Asn | missense_variant | 1/11 | 1 | NM_005309.3 | P1 | |
ENST00000527086.1 | n.187+621G>T | intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes AF: 0.417 AC: 63355AN: 152052Hom.: 14299 Cov.: 35
GnomAD3 exomes AF: 0.482 AC: 119112AN: 247036Hom.: 29518 AF XY: 0.487 AC XY: 65323AN XY: 134238
GnomAD4 exome AF: 0.471 AC: 687172AN: 1458008Hom.: 164156 Cov.: 56 AF XY: 0.475 AC XY: 344635AN XY: 725480
GnomAD4 genome AF: 0.417 AC: 63383AN: 152170Hom.: 14304 Cov.: 35 AF XY: 0.423 AC XY: 31450AN XY: 74402
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at