4-151712515-C-T

Variant names:

• chr4-151712515-C-T
• rs1355413
• NM_004564.3:c.763+3494G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_004564.3(GATB):​c.763+3494G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.584 in 151,998 control chromosomes in the GnomAD database, including 28,259 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.58 (28259 hom., cov: 32)
• Consequence: GATB NM_004564.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0190
• Publications: 3 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.85 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GATB	NM_004564.3	c.763+3494G>A		intron_variant	Intron 5 of 12	ENST00000263985.11	NP_004555.1
GATB	NM_001363341.2	c.763+3494G>A		intron_variant	Intron 5 of 11		NP_001350270.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GATB	ENST00000263985.11	c.763+3494G>A		intron_variant	Intron 5 of 12	1	NM_004564.3	ENSP00000263985.6

Frequencies

GnomAD3 genomes AF: 0.584 AC: 88649 AN: 151880 Hom.: 28209 Cov.: 32

Gnomad AFR AF: 0.857

Gnomad AMI AF: 0.355

Gnomad AMR AF: 0.446

Gnomad ASJ AF: 0.487

Gnomad EAS AF: 0.467

Gnomad SAS AF: 0.610

Gnomad FIN AF: 0.464

Gnomad MID AF: 0.544

Gnomad NFE AF: 0.482

Gnomad OTH AF: 0.573

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

GnomAD4 genome AF: 0.584 AC: 88749 AN: 151998 Hom.: 28259 Cov.: 32 AF XY: 0.579 AC XY: 43003 AN XY: 74278

African (AFR) AF: 0.857 AC: 35587 AN: 41506

American (AMR) AF: 0.445 AC: 6807 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.487 AC: 1687 AN: 3464

East Asian (EAS) AF: 0.467 AC: 2400 AN: 5142

South Asian (SAS) AF: 0.607 AC: 2920 AN: 4808

European-Finnish (FIN) AF: 0.464 AC: 4894 AN: 10552

Middle Eastern (MID) AF: 0.548 AC: 161 AN: 294

European-Non Finnish (NFE) AF: 0.482 AC: 32759 AN: 67936

Other (OTH) AF: 0.575 AC: 1212 AN: 2106

Alfa AF: 0.554 Hom.: 3104

Bravo AF: 0.589

Asia WGS AF: 0.553 AC: 1925 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	7.3
DANN	Benign	0.52
PhyloP100		-0.019
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1355413; hg19: chr4-152633667;