Variant 10-121790176-T-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BA1

The NM_001001976.3(ATE1):c.1371A>C(p.Pro457=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.454 in 1,613,526 control chromosomes in the GnomAD database, including 167,379 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.46 ( 16319 hom., cov: 32)

Exomes 𝑓: 0.45 ( 151060 hom. )

Consequence

ATE1
NM_001001976.3 synonymous

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: -1.43

Variant links:

Genes affected

ATE1 (HGNC:782): (arginyltransferase 1) This gene encodes an arginyltransferase, an enzyme that is involved in posttranslational conjugation of arginine to N-terminal aspartate or glutamate residues. Conjugation of arginine to the N-terminal aspartate or glutamate targets proteins for ubiquitin-dependent degradation. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2013]

ATE1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.72).

BP6

Variant 10-121790176-T-G is Benign according to our data. Variant chr10-121790176-T-G is described in ClinVar as [Benign]. Clinvar id is 3060412.Status of the report is no_assertion_criteria_provided, 0 stars.

BP7

Synonymous conserved (PhyloP=-1.43 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.54 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ATE1	NM_001001976.3 linkuse as main transcript	c.1371A>C	p.Pro457=	synonymous_variant	11/12	ENST00000224652.12	NP_001001976.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ATE1	ENST00000224652.12 linkuse as main transcript	c.1371A>C	p.Pro457=	synonymous_variant	11/12	1	NM_001001976.3	ENSP00000224652	A1	O95260-1

Frequencies

GnomAD3 genomes

AF:

0.463

AC:

70279

AN:

151852

Hom.:

16314

Cov.:

show subpopulations

Gnomad AFR

AF:

0.464

Gnomad AMI

AF:

0.489

Gnomad AMR

AF:

0.468

Gnomad ASJ

AF:

0.389

Gnomad EAS

AF:

0.557

Gnomad SAS

AF:

0.533

Gnomad FIN

AF:

0.474

Gnomad MID

AF:

0.421

Gnomad NFE

AF:

0.451

Gnomad OTH

AF:

0.462

GnomAD3 exomes

AF:

0.468

AC:

117508

AN:

251248

Hom.:

27763

AF XY:

0.470

AC XY:

63840

AN XY:

135782

show subpopulations

Gnomad AFR exome

AF:

0.466

Gnomad AMR exome

AF:

0.452

Gnomad ASJ exome

AF:

0.384

Gnomad EAS exome

AF:

0.555

Gnomad SAS exome

AF:

0.530

Gnomad FIN exome

AF:

0.464

Gnomad NFE exome

AF:

0.450

Gnomad OTH exome

AF:

0.461

GnomAD4 exome

AF:

0.453

AC:

662198

AN:

1461556

Hom.:

151060

Cov.:

AF XY:

0.455

AC XY:

330680

AN XY:

727094

show subpopulations

Gnomad4 AFR exome

AF:

0.465

Gnomad4 AMR exome

AF:

0.454

Gnomad4 ASJ exome

AF:

0.388

Gnomad4 EAS exome

AF:

0.545

Gnomad4 SAS exome

AF:

0.523

Gnomad4 FIN exome

AF:

0.468

Gnomad4 NFE exome

AF:

0.445

Gnomad4 OTH exome

AF:

0.452

GnomAD4 genome

AF:

0.463

AC:

70320

AN:

151970

Hom.:

16319

Cov.:

AF XY:

0.464

AC XY:

34475

AN XY:

74262

show subpopulations

Gnomad4 AFR

AF:

0.463

Gnomad4 AMR

AF:

0.469

Gnomad4 ASJ

AF:

0.389

Gnomad4 EAS

AF:

0.557

Gnomad4 SAS

AF:

0.533

Gnomad4 FIN

AF:

0.474

Gnomad4 NFE

AF:

0.451

Gnomad4 OTH

AF:

0.459

Alfa

AF:

0.434

Hom.:

9492

Bravo

AF:

0.461

Asia WGS

AF:

0.519

AC:

1801

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

ATE1-related disorder

Benign:1

Benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Oct 17, 2019

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.72

CADD

Benign

0.99

DANN

Benign

0.64

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

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