4-151688846-C-CA

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_004564.3(GATB):c.1198-84_1198-83insT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.379 in 1,381,190 control chromosomes in the GnomAD database, including 102,552 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.40 (12631 hom., cov: 0)
  • Exomes 𝑓: 0.38 (89921 hom.)
• Consequence: GATB NM_004564.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.0890

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 -10 ACMG points.

• BP6: Variant 4-151688846-C-CA is Benign according to our data. Variant chr4-151688846-C-CA is described in ClinVar as [Benign]. Clinvar id is 1273897.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.56 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GATB	NM_004564.3	c.1198-84_1198-83insT		intron_variant		ENST00000263985.11
GATB	NM_001363341.2	c.1198-84_1198-83insT		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GATB	ENST00000263985.11	c.1198-84_1198-83insT		intron_variant		1	NM_004564.3	P1

Frequencies

GnomAD3 genomes AF: 0.402 AC: 60964 AN: 151764 Hom.: 12614 Cov.: 0

Gnomad AFR AF: 0.491

Gnomad AMI AF: 0.213

Gnomad AMR AF: 0.338

Gnomad ASJ AF: 0.377

Gnomad EAS AF: 0.360

Gnomad SAS AF: 0.579

Gnomad FIN AF: 0.366

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.361

Gnomad OTH AF: 0.421

GnomAD4 exome AF: 0.376 AC: 462409 AN: 1229308 Hom.: 89921 AF XY: 0.383 AC XY: 234664 AN XY: 613016

Gnomad4 AFR exome AF: 0.494

Gnomad4 AMR exome AF: 0.291

Gnomad4 ASJ exome AF: 0.383

Gnomad4 EAS exome AF: 0.397

Gnomad4 SAS exome AF: 0.587

Gnomad4 FIN exome AF: 0.363

Gnomad4 NFE exome AF: 0.359

Gnomad4 OTH exome AF: 0.387

GnomAD4 genome AF: 0.402 AC: 61020 AN: 151882 Hom.: 12631 Cov.: 0 AF XY: 0.404 AC XY: 29997 AN XY: 74232

Gnomad4 AFR AF: 0.491

Gnomad4 AMR AF: 0.338

Gnomad4 ASJ AF: 0.377

Gnomad4 EAS AF: 0.360

Gnomad4 SAS AF: 0.578

Gnomad4 FIN AF: 0.366

Gnomad4 NFE AF: 0.361

Gnomad4 OTH AF: 0.424

Alfa AF: 0.318 Hom.: 286

Asia WGS AF: 0.447 AC: 1555 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

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: rs11390610; hg19: chr4-152609998;