16-58709497-T-C
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Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_002080.4(GOT2):āc.1090A>Gā(p.Lys364Glu) variant causes a missense change. The variant allele was found at a frequency of 0.000259 in 1,613,934 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ).
Frequency
Genomes: š 0.00032 ( 0 hom., cov: 33)
Exomes š: 0.00025 ( 1 hom. )
Consequence
GOT2
NM_002080.4 missense
NM_002080.4 missense
Scores
1
8
10
Clinical Significance
Conservation
PhyloP100: 4.92
Genes affected
GOT2 (HGNC:4433): (glutamic-oxaloacetic transaminase 2) Glutamic-oxaloacetic transaminase is a pyridoxal phosphate-dependent enzyme which exists in cytoplasmic and inner-membrane mitochondrial forms, GOT1 and GOT2, respectively. GOT plays a role in amino acid metabolism and the urea and tricarboxylic acid cycles. The two enzymes are homodimeric and show close homology. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2013]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.010149479).
BP6
Variant 16-58709497-T-C is Benign according to our data. Variant chr16-58709497-T-C is described in ClinVar as [Benign]. Clinvar id is 2064625.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GOT2 | NM_002080.4 | c.1090A>G | p.Lys364Glu | missense_variant | 9/10 | ENST00000245206.10 | |
GOT2 | NM_001286220.2 | c.961A>G | p.Lys321Glu | missense_variant | 8/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GOT2 | ENST00000245206.10 | c.1090A>G | p.Lys364Glu | missense_variant | 9/10 | 1 | NM_002080.4 | P1 | |
GOT2 | ENST00000434819.2 | c.961A>G | p.Lys321Glu | missense_variant | 8/9 | 2 | |||
GOT2 | ENST00000494627.1 | n.441A>G | non_coding_transcript_exon_variant | 2/2 | 2 |
Frequencies
GnomAD3 genomes AF: 0.000315 AC: 48AN: 152198Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.000767 AC: 193AN: 251466Hom.: 0 AF XY: 0.000647 AC XY: 88AN XY: 135908
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GnomAD4 exome AF: 0.000253 AC: 370AN: 1461618Hom.: 1 Cov.: 30 AF XY: 0.000223 AC XY: 162AN XY: 727108
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GnomAD4 genome AF: 0.000315 AC: 48AN: 152316Hom.: 0 Cov.: 33 AF XY: 0.000389 AC XY: 29AN XY: 74476
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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 | Jul 17, 2023 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Uncertain
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Uncertain
T;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D;D
M_CAP
Benign
D
MetaRNN
Benign
T;T
MetaSVM
Uncertain
T
MutationAssessor
Benign
L;.
MutationTaster
Benign
D;D
PrimateAI
Uncertain
T
PROVEAN
Uncertain
D;D
REVEL
Uncertain
Sift
Benign
T;T
Sift4G
Benign
T;T
Polyphen
B;.
Vest4
MVP
MPC
ClinPred
T
GERP RS
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gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at