4-151688965-T-C

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_004564.3(GATB):c.1198-202A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.563 in 151,972 control chromosomes in the GnomAD database, including 25,613 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.56 (25613 hom., cov: 32)
• Consequence: GATB NM_004564.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -5.35

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]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BP6: Variant 4-151688965-T-C is Benign according to our data. Variant chr4-151688965-T-C is described in ClinVar as [Benign]. Clinvar id is 1287289.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.775 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GATB	NM_004564.3	c.1198-202A>G		intron_variant		ENST00000263985.11
GATB	NM_001363341.2	c.1198-202A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GATB	ENST00000263985.11	c.1198-202A>G		intron_variant		1	NM_004564.3	P1

Frequencies

GnomAD3 genomes AF: 0.563 AC: 85422 AN: 151854 Hom.: 25570 Cov.: 32

Gnomad AFR AF: 0.782

Gnomad AMI AF: 0.354

Gnomad AMR AF: 0.439

Gnomad ASJ AF: 0.487

Gnomad EAS AF: 0.468

Gnomad SAS AF: 0.613

Gnomad FIN AF: 0.464

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.482

Gnomad OTH AF: 0.561

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.563 AC: 85513 AN: 151972 Hom.: 25613 Cov.: 32 AF XY: 0.558 AC XY: 41469 AN XY: 74270

Gnomad4 AFR AF: 0.782

Gnomad4 AMR AF: 0.438

Gnomad4 ASJ AF: 0.487

Gnomad4 EAS AF: 0.468

Gnomad4 SAS AF: 0.611

Gnomad4 FIN AF: 0.464

Gnomad4 NFE AF: 0.482

Gnomad4 OTH AF: 0.564

Alfa AF: 0.513 Hom.: 10443

Bravo AF: 0.565

Asia WGS AF: 0.551 AC: 1916 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 12, 2021

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.0070
Dann	Benign	0.32

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs3749561; hg19: chr4-152610117;