Genetic Variant ENST00000514269.1:n.906T>C (chr4-151675388-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000514269.1(ENSG00000251455):n.906T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.602 in 152,476 control chromosomes in the GnomAD database, including 30,150 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 0.60 ( 30074 hom., cov: 32)

Exomes 𝑓: 0.58 ( 76 hom. )

Consequence

ENSG00000251455
ENST00000514269.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.796

Publications

3 publications found

Variant links:

Genes affected

ENSG00000251455 (HGNC:):

ENSG00000251455 links:

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]

GATB links:

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ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.92).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.881 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
GATB	NM_004564.3 link	c.1411-2492A>G	intron_variant	Intron 11 of 12	ENST00000263985.11	NP_004555.1	O75879
LOC107986197	XR_001741447.3 link	n.3800T>C	non_coding_transcript_exon_variant	Exon 1 of 2
GATB	NM_001363341.2 link	c.1411-4086A>G	intron_variant	Intron 11 of 11		NP_001350270.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GATB	ENST00000263985.11 link	c.1411-2492A>G		intron_variant	Intron 11 of 12	1	NM_004564.3	ENSP00000263985.6		O75879

Frequencies

GnomAD3 genomes

AF:

0.601

AC:

91388

AN:

151938

Hom.:

30024

Cov.:

show subpopulations

Gnomad AFR

AF:

0.889

Gnomad AMI

AF:

0.391

Gnomad AMR

AF:

0.487

Gnomad ASJ

AF:

0.484

Gnomad EAS

AF:

0.490

Gnomad SAS

AF:

0.617

Gnomad FIN

AF:

0.472

Gnomad MID

AF:

0.580

Gnomad NFE

AF:

0.489

Gnomad OTH

AF:

0.584

GnomAD4 exome

AF:

0.581

AC:

244

AN:

420

Hom.:

Cov.:

AF XY:

0.570

AC XY:

180

AN XY:

316

show subpopulations

African (AFR)

AF:

0.917

AC:

AN:

American (AMR)

AF:

0.500

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.375

AC:

AN:

East Asian (EAS)

AF:

0.800

AC:

AN:

South Asian (SAS)

AF:

1.00

AC:

AN:

European-Finnish (FIN)

AF:

0.500

AC:

AN:

Middle Eastern (MID)

AF:

1.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.537

AC:

187

AN:

348

Other (OTH)

AF:

0.917

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.515

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.602

AC:

91492

AN:

152056

Hom.:

30074

Cov.:

AF XY:

0.597

AC XY:

44375

AN XY:

74312

show subpopulations

African (AFR)

AF:

0.889

AC:

36881

AN:

41500

American (AMR)

AF:

0.487

AC:

7442

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.484

AC:

1680

AN:

3472

East Asian (EAS)

AF:

0.490

AC:

2526

AN:

5156

South Asian (SAS)

AF:

0.615

AC:

2963

AN:

4816

European-Finnish (FIN)

AF:

0.472

AC:

4987

AN:

10574

Middle Eastern (MID)

AF:

0.579

AC:

168

AN:

290

European-Non Finnish (NFE)

AF:

0.489

AC:

33254

AN:

67936

Other (OTH)

AF:

0.586

AC:

1236

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1637

3274

4911

6548

8185

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

732

1464

2196

2928

3660

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.577

Hom.:

3508

Bravo

AF:

0.609

Asia WGS

AF:

0.566

AC:

1969

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

2.3

(source)

DANN

Benign

0.69

PhyloP100

-0.80

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over