chr8-144504336-C-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_005309.3(GPT):c.32C>A(p.Ala11Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00166 in 1,610,528 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_005309.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GPT | NM_005309.3 | c.32C>A | p.Ala11Glu | missense_variant | 1/11 | ENST00000394955.3 | |
LOC101928953 | XR_007061149.1 | n.103+1036G>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GPT | ENST00000394955.3 | c.32C>A | p.Ala11Glu | missense_variant | 1/11 | 1 | NM_005309.3 | P1 | |
ENST00000527086.1 | n.187+629G>T | intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.00132 AC: 201AN: 152250Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00109 AC: 269AN: 247264Hom.: 1 AF XY: 0.00108 AC XY: 145AN XY: 134414
GnomAD4 exome AF: 0.00170 AC: 2474AN: 1458160Hom.: 3 Cov.: 30 AF XY: 0.00158 AC XY: 1150AN XY: 725564
GnomAD4 genome ? AF: 0.00132 AC: 201AN: 152368Hom.: 0 Cov.: 33 AF XY: 0.00119 AC XY: 89AN XY: 74504
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at