rs11076256
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_002080.4(GOT2):c.562G>A(p.Gly188Ser) variant causes a missense change. The variant allele was found at a frequency of 0.0736 in 1,596,714 control chromosomes in the GnomAD database, including 4,759 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Genomes: 𝑓 0.057 ( 299 hom., cov: 33)
Exomes 𝑓: 0.075 ( 4460 hom. )
Consequence
GOT2
NM_002080.4 missense
NM_002080.4 missense
Scores
1
7
10
Clinical Significance
Conservation
PhyloP100: 6.04
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 Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.0035402477).
BP6
?
Variant 16-58718562-C-T is Benign according to our data. Variant chr16-58718562-C-T is described in ClinVar as [Benign]. Clinvar id is 1555382.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0793 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GOT2 | NM_002080.4 | c.562G>A | p.Gly188Ser | missense_variant | 5/10 | ENST00000245206.10 | |
GOT2 | NM_001286220.2 | c.433G>A | p.Gly145Ser | missense_variant | 4/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GOT2 | ENST00000245206.10 | c.562G>A | p.Gly188Ser | missense_variant | 5/10 | 1 | NM_002080.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0572 AC: 8704AN: 152120Hom.: 299 Cov.: 33
GnomAD3 genomes
?
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GnomAD3 exomes AF: 0.0612 AC: 14703AN: 240202Hom.: 575 AF XY: 0.0647 AC XY: 8393AN XY: 129720
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GnomAD4 exome AF: 0.0754 AC: 108880AN: 1444476Hom.: 4460 Cov.: 32 AF XY: 0.0757 AC XY: 54275AN XY: 716772
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GnomAD4 genome ? AF: 0.0571 AC: 8695AN: 152238Hom.: 299 Cov.: 33 AF XY: 0.0563 AC XY: 4187AN XY: 74432
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315
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329
ESP6500AA
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139
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680
ExAC
?
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7684
Asia WGS
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180
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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 | Jan 30, 2024 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Uncertain
Dann
Uncertain
DEOGEN2
Uncertain
D;.
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T;T
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationAssessor
Uncertain
M;.
MutationTaster
Benign
D;D
PrimateAI
Benign
T
PROVEAN
Pathogenic
D;D
REVEL
Uncertain
Sift
Benign
D;D
Sift4G
Benign
T;T
Polyphen
P;.
Vest4
MPC
ClinPred
T
GERP RS
Varity_R
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