chr4-151688674-A-C
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The NM_004564.3(GATB):c.1287T>G(p.Thr429=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0347 in 1,612,322 control chromosomes in the GnomAD database, including 1,084 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.025 ( 66 hom., cov: 31)
Exomes 𝑓: 0.036 ( 1018 hom. )
Consequence
GATB
NM_004564.3 synonymous
NM_004564.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.275
Genes affected
GATB (HGNC:8849): (glutamyl-tRNA amidotransferase subunit B) Enables glutaminyl-tRNA synthase (glutamine-hydrolyzing) activity. Involved in glutaminyl-tRNAGln biosynthesis via transamidation and mitochondrial translation. Located in mitochondrion. Part of glutamyl-tRNA(Gln) amidotransferase complex. Implicated in combined oxidative phosphorylation deficiency 41. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -15 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BP6
?
Variant 4-151688674-A-C is Benign according to our data. Variant chr4-151688674-A-C is described in ClinVar as [Benign]. Clinvar id is 3056173.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=0.275 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0252 (3837/152196) while in subpopulation NFE AF= 0.0407 (2766/68010). AF 95% confidence interval is 0.0394. There are 66 homozygotes in gnomad4. There are 1703 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 65 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GATB | NM_004564.3 | c.1287T>G | p.Thr429= | synonymous_variant | 10/13 | ENST00000263985.11 | |
GATB | NM_001363341.2 | c.1287T>G | p.Thr429= | synonymous_variant | 10/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GATB | ENST00000263985.11 | c.1287T>G | p.Thr429= | synonymous_variant | 10/13 | 1 | NM_004564.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0252 AC: 3834AN: 152078Hom.: 65 Cov.: 31
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GnomAD3 exomes AF: 0.0263 AC: 6568AN: 249644Hom.: 111 AF XY: 0.0266 AC XY: 3586AN XY: 134844
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GnomAD4 exome AF: 0.0357 AC: 52153AN: 1460126Hom.: 1018 Cov.: 32 AF XY: 0.0350 AC XY: 25448AN XY: 726230
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GnomAD4 genome ? AF: 0.0252 AC: 3837AN: 152196Hom.: 66 Cov.: 31 AF XY: 0.0229 AC XY: 1703AN XY: 74388
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
GATB-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Nov 25, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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BayesDel_noAF
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Cadd
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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