Variant 12-120446525-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BA1

The NM_176818.3(GATC):c.45C>T(p.Gly15Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.312 in 1,601,406 control chromosomes in the GnomAD database, including 81,272 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.26 ( 5893 hom., cov: 33)

Exomes 𝑓: 0.32 ( 75379 hom. )

Consequence

GATC
NM_176818.3 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.353

Variant links:

Genes affected

GATC (HGNC:25068): (glutamyl-tRNA amidotransferase subunit C) 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 42. [provided by Alliance of Genome Resources, Apr 2022]

GATC links:

ENSG00000111780 (HGNC:):

ENSG00000111780 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -19 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.21).

BP6

Variant 12-120446525-C-T is Benign according to our data. Variant chr12-120446525-C-T is described in ClinVar as [Benign]. Clinvar id is 1246559.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.353 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.479 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GATC	NM_176818.3 linkuse as main transcript	c.45C>T	p.Gly15Gly	synonymous_variant	1/4	ENST00000551765.6	NP_789788.1	O43716
GATC	NR_033684.2 linkuse as main transcript	n.82C>T		non_coding_transcript_exon_variant	1/5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
GATC	ENST00000551765.6 linkuse as main transcript	c.45C>T	p.Gly15Gly	synonymous_variant	1/4	1	NM_176818.3	ENSP00000446872.1	O43716
ENSG00000111780	ENST00000551806.1 linkuse as main transcript	c.175-132C>T		intron_variant		3		ENSP00000450281.1	H0YIV9
GATC	ENST00000548171.1 linkuse as main transcript	n.45C>T		non_coding_transcript_exon_variant	1/5	2		ENSP00000448397.1	F8VRU3

Frequencies

GnomAD3 genomes

AF:

0.258

AC:

39125

AN:

151870

Hom.:

5881

Cov.:

show subpopulations

Gnomad AFR

AF:

0.109

Gnomad AMI

AF:

0.245

Gnomad AMR

AF:

0.272

Gnomad ASJ

AF:

0.227

Gnomad EAS

AF:

0.495

Gnomad SAS

AF:

0.283

Gnomad FIN

AF:

0.331

Gnomad MID

AF:

0.209

Gnomad NFE

AF:

0.317

Gnomad OTH

AF:

0.247

GnomAD3 exomes

AF:

0.300

AC:

73308

AN:

244514

Hom.:

11924

AF XY:

0.301

AC XY:

39968

AN XY:

132564

show subpopulations

Gnomad AFR exome

AF:

0.102

Gnomad AMR exome

AF:

0.295

Gnomad ASJ exome

AF:

0.224

Gnomad EAS exome

AF:

0.492

Gnomad SAS exome

AF:

0.286

Gnomad FIN exome

AF:

0.320

Gnomad NFE exome

AF:

0.306

Gnomad OTH exome

AF:

0.290

GnomAD4 exome

AF:

0.318

AC:

460573

AN:

1449418

Hom.:

75379

Cov.:

AF XY:

0.317

AC XY:

228330

AN XY:

719778

show subpopulations

Gnomad4 AFR exome

AF:

0.0998

Gnomad4 AMR exome

AF:

0.292

Gnomad4 ASJ exome

AF:

0.229

Gnomad4 EAS exome

AF:

0.497

Gnomad4 SAS exome

AF:

0.289

Gnomad4 FIN exome

AF:

0.316

Gnomad4 NFE exome

AF:

0.324

Gnomad4 OTH exome

AF:

0.306

GnomAD4 genome

AF:

0.258

AC:

39149

AN:

151988

Hom.:

5893

Cov.:

AF XY:

0.261

AC XY:

19372

AN XY:

74278

show subpopulations

Gnomad4 AFR

AF:

0.108

Gnomad4 AMR

AF:

0.273

Gnomad4 ASJ

AF:

0.227

Gnomad4 EAS

AF:

0.495

Gnomad4 SAS

AF:

0.284

Gnomad4 FIN

AF:

0.331

Gnomad4 NFE

AF:

0.317

Gnomad4 OTH

AF:

0.244

Alfa

AF:

0.295

Hom.:

7388

Bravo

AF:

0.248

Asia WGS

AF:

0.346

AC:

1206

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	May 04, 2021	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.21

CADD

Benign

8.5

DANN

Benign

0.84

RBP_binding_hub_radar

0.92

RBP_regulation_power_radar

2.0

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.040

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over