Variant 10-121836739-T-C 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.1236A>G(p.Ser412=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.913 in 1,575,284 control chromosomes in the GnomAD database, including 657,356 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.90 ( 61808 hom., cov: 32)

Exomes 𝑓: 0.91 ( 595548 hom. )

Consequence

ATE1
NM_001001976.3 synonymous

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: -1.59

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=-0.84).

BP6

Variant 10-121836739-T-C is Benign according to our data. Variant chr10-121836739-T-C is described in ClinVar as [Benign]. Clinvar id is 3060294.Status of the report is no_assertion_criteria_provided, 0 stars.

BP7

Synonymous conserved (PhyloP=-1.59 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.918 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.1236A>G	p.Ser412=	synonymous_variant	10/12	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.1236A>G	p.Ser412=	synonymous_variant	10/12	1	NM_001001976.3	ENSP00000224652	A1	O95260-1

Frequencies

GnomAD3 genomes

AF:

0.900

AC:

136883

AN:

152092

Hom.:

61770

Cov.:

show subpopulations

Gnomad AFR

AF:

0.871

Gnomad AMI

AF:

0.954

Gnomad AMR

AF:

0.822

Gnomad ASJ

AF:

0.953

Gnomad EAS

AF:

0.931

Gnomad SAS

AF:

0.891

Gnomad FIN

AF:

0.931

Gnomad MID

AF:

0.968

Gnomad NFE

AF:

0.924

Gnomad OTH

AF:

0.905

GnomAD3 exomes

AF:

0.896

AC:

209383

AN:

233738

Hom.:

94265

AF XY:

0.901

AC XY:

114024

AN XY:

126538

show subpopulations

Gnomad AFR exome

AF:

0.862

Gnomad AMR exome

AF:

0.759

Gnomad ASJ exome

AF:

0.950

Gnomad EAS exome

AF:

0.934

Gnomad SAS exome

AF:

0.887

Gnomad FIN exome

AF:

0.928

Gnomad NFE exome

AF:

0.922

Gnomad OTH exome

AF:

0.915

GnomAD4 exome

AF:

0.914

AC:

1301050

AN:

1423074

Hom.:

595548

Cov.:

AF XY:

0.914

AC XY:

647858

AN XY:

708492

show subpopulations

Gnomad4 AFR exome

AF:

0.871

Gnomad4 AMR exome

AF:

0.767

Gnomad4 ASJ exome

AF:

0.952

Gnomad4 EAS exome

AF:

0.923

Gnomad4 SAS exome

AF:

0.890

Gnomad4 FIN exome

AF:

0.931

Gnomad4 NFE exome

AF:

0.921

Gnomad4 OTH exome

AF:

0.914

GnomAD4 genome

AF:

0.900

AC:

136976

AN:

152210

Hom.:

61808

Cov.:

AF XY:

0.899

AC XY:

66901

AN XY:

74418

show subpopulations

Gnomad4 AFR

AF:

0.872

Gnomad4 AMR

AF:

0.822

Gnomad4 ASJ

AF:

0.953

Gnomad4 EAS

AF:

0.931

Gnomad4 SAS

AF:

0.891

Gnomad4 FIN

AF:

0.931

Gnomad4 NFE

AF:

0.924

Gnomad4 OTH

AF:

0.903

Alfa

AF:

0.916

Hom.:

80944

Bravo

AF:

0.889

Asia WGS

AF:

0.881

AC:

3060

AN:

3470

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

-0.84

CADD

Benign

2.2

DANN

Benign

0.60

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