16-58709462-G-A
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_002080.4(GOT2):c.1125C>T(p.Thr375=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000851 in 1,613,782 control chromosomes in the GnomAD database, including 9 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0043 ( 5 hom., cov: 33)
Exomes 𝑓: 0.00049 ( 4 hom. )
Consequence
GOT2
NM_002080.4 synonymous
NM_002080.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.767
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 (BayesDel_noAF=-0.66).
BP6
Variant 16-58709462-G-A is Benign according to our data. Variant chr16-58709462-G-A is described in ClinVar as [Benign]. Clinvar id is 1614801.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
Variant frequency is greater than expected in population afr. gnomad4_exome allele frequency = 0.000489 (714/1461492) while in subpopulation AFR AF= 0.0172 (577/33478). AF 95% confidence interval is 0.0161. There are 4 homozygotes in gnomad4_exome. There are 321 alleles in male gnomad4_exome subpopulation. Median coverage is 31. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 5 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GOT2 | NM_002080.4 | c.1125C>T | p.Thr375= | synonymous_variant | 9/10 | ENST00000245206.10 | |
GOT2 | NM_001286220.2 | c.996C>T | p.Thr332= | synonymous_variant | 8/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GOT2 | ENST00000245206.10 | c.1125C>T | p.Thr375= | synonymous_variant | 9/10 | 1 | NM_002080.4 | P1 | |
GOT2 | ENST00000434819.2 | c.996C>T | p.Thr332= | synonymous_variant | 8/9 | 2 | |||
GOT2 | ENST00000494627.1 | n.476C>T | non_coding_transcript_exon_variant | 2/2 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00432 AC: 658AN: 152172Hom.: 5 Cov.: 33
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GnomAD3 exomes AF: 0.00115 AC: 288AN: 251450Hom.: 3 AF XY: 0.000927 AC XY: 126AN XY: 135892
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GnomAD4 exome AF: 0.000489 AC: 714AN: 1461492Hom.: 4 Cov.: 31 AF XY: 0.000442 AC XY: 321AN XY: 727016
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GnomAD4 genome AF: 0.00433 AC: 659AN: 152290Hom.: 5 Cov.: 33 AF XY: 0.00411 AC XY: 306AN XY: 74462
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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 22, 2024 | - - |
Computational scores
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BayesDel_noAF
Benign
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Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at