Variant 10-121743672-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BA1

The NM_001001976.3(ATE1):c.*8A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.15 in 1,597,688 control chromosomes in the GnomAD database, including 24,133 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.23 ( 5647 hom., cov: 32)

Exomes 𝑓: 0.14 ( 18486 hom. )

Consequence

ATE1
NM_001001976.3 3_prime_UTR

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: -2.93

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 -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BP6

Variant 10-121743672-T-C is Benign according to our data. Variant chr10-121743672-T-C is described in ClinVar as [Benign]. Clinvar id is 3059476.Status of the report is no_assertion_criteria_provided, 0 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.433 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ATE1	NM_001001976.3 linkuse as main transcript	c.*8A>G		3_prime_UTR_variant	12/12	ENST00000224652.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ATE1	ENST00000224652.12 linkuse as main transcript	c.*8A>G		3_prime_UTR_variant	12/12	1	NM_001001976.3	A1	O95260-1

Frequencies

GnomAD3 genomes

AF:

0.234

AC:

35538

AN:

151886

Hom.:

5631

Cov.:

show subpopulations

Gnomad AFR

AF:

0.438

Gnomad AMI

AF:

0.216

Gnomad AMR

AF:

0.302

Gnomad ASJ

AF:

0.143

Gnomad EAS

AF:

0.0727

Gnomad SAS

AF:

0.232

Gnomad FIN

AF:

0.194

Gnomad MID

AF:

0.161

Gnomad NFE

AF:

0.120

Gnomad OTH

AF:

0.197

GnomAD3 exomes

AF:

0.192

AC:

45791

AN:

238390

Hom.:

6063

AF XY:

0.182

AC XY:

23499

AN XY:

128860

show subpopulations

Gnomad AFR exome

AF:

0.446

Gnomad AMR exome

AF:

0.367

Gnomad ASJ exome

AF:

0.139

Gnomad EAS exome

AF:

0.0658

Gnomad SAS exome

AF:

0.224

Gnomad FIN exome

AF:

0.189

Gnomad NFE exome

AF:

0.123

Gnomad OTH exome

AF:

0.162

GnomAD4 exome

AF:

0.141

AC:

203411

AN:

1445684

Hom.:

18486

Cov.:

AF XY:

0.141

AC XY:

101414

AN XY:

718202

show subpopulations

Gnomad4 AFR exome

AF:

0.457

Gnomad4 AMR exome

AF:

0.359

Gnomad4 ASJ exome

AF:

0.137

Gnomad4 EAS exome

AF:

0.0705

Gnomad4 SAS exome

AF:

0.223

Gnomad4 FIN exome

AF:

0.186

Gnomad4 NFE exome

AF:

0.116

Gnomad4 OTH exome

AF:

0.159

GnomAD4 genome

AF:

0.234

AC:

35608

AN:

152004

Hom.:

5647

Cov.:

AF XY:

0.237

AC XY:

17592

AN XY:

74292

show subpopulations

Gnomad4 AFR

AF:

0.438

Gnomad4 AMR

AF:

0.302

Gnomad4 ASJ

AF:

0.143

Gnomad4 EAS

AF:

0.0725

Gnomad4 SAS

AF:

0.231

Gnomad4 FIN

AF:

0.194

Gnomad4 NFE

AF:

0.120

Gnomad4 OTH

AF:

0.207

Alfa

AF:

0.137

Hom.:

755

Bravo

AF:

0.251

Asia WGS

AF:

0.206

AC:

715

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 28, 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

-0.90

CADD

Benign

0.95

DANN

Benign

0.76

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