8-144504672-G-A
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_005309.3(GPT):c.231G>A(p.Arg77=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000832 in 1,613,276 control chromosomes in the GnomAD database, including 17 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0042 ( 9 hom., cov: 34)
Exomes 𝑓: 0.00048 ( 8 hom. )
Consequence
GPT
NM_005309.3 synonymous
NM_005309.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.137
Genes affected
GPT (HGNC:4552): (glutamic--pyruvic transaminase) This gene encodes cytosolic alanine aminotransaminase 1 (ALT1); also known as glutamate-pyruvate transaminase 1. This enzyme catalyzes the reversible transamination between alanine and 2-oxoglutarate to generate pyruvate and glutamate and, therefore, plays a key role in the intermediary metabolism of glucose and amino acids. Serum activity levels of this enzyme are routinely used as a biomarker of liver injury caused by drug toxicity, infection, alcohol, and steatosis. A related gene on chromosome 16 encodes a putative mitochondrial alanine aminotransaminase.[provided by RefSeq, Nov 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.72).
BP6
?
Variant 8-144504672-G-A is Benign according to our data. Variant chr8-144504672-G-A is described in ClinVar as [Benign]. Clinvar id is 710602.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-0.137 with no splicing effect.
BS2
?
High Homozygotes in GnomAd at 7 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GPT | NM_005309.3 | c.231G>A | p.Arg77= | synonymous_variant | 2/11 | ENST00000394955.3 | |
LOC101928953 | XR_007061149.1 | n.103+700C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GPT | ENST00000394955.3 | c.231G>A | p.Arg77= | synonymous_variant | 2/11 | 1 | NM_005309.3 | P1 | |
ENST00000527086.1 | n.187+293C>T | intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.00417 AC: 635AN: 152182Hom.: 7 Cov.: 34
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GnomAD3 exomes AF: 0.00109 AC: 274AN: 251138Hom.: 0 AF XY: 0.000773 AC XY: 105AN XY: 135850
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GnomAD4 exome AF: 0.000476 AC: 695AN: 1460976Hom.: 8 Cov.: 35 AF XY: 0.000442 AC XY: 321AN XY: 726770
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GnomAD4 genome ? AF: 0.00425 AC: 647AN: 152300Hom.: 9 Cov.: 34 AF XY: 0.00404 AC XY: 301AN XY: 74464
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Oct 24, 2018 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at