Variant chr1-212619561-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2

The NM_001674.4(ATF3):c.*6C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00684 in 1,613,840 control chromosomes in the GnomAD database, including 51 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.0054 ( 4 hom., cov: 32)

Exomes 𝑓: 0.0070 ( 47 hom. )

Consequence

ATF3
NM_001674.4 3_prime_UTR

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: -1.17

Variant links:

Genes affected

ATF3 (HGNC:785): (activating transcription factor 3) This gene encodes a member of the mammalian activation transcription factor/cAMP responsive element-binding (CREB) protein family of transcription factors. This gene is induced by a variety of signals, including many of those encountered by cancer cells, and is involved in the complex process of cellular stress response. Multiple transcript variants encoding different isoforms have been found for this gene. It is possible that alternative splicing of this gene may be physiologically important in the regulation of target genes. [provided by RefSeq, Apr 2011]

ATF3 links:

ATF3 (HGNC:):

ATF3 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BP6

Variant 1-212619561-C-T is Benign according to our data. Variant chr1-212619561-C-T is described in ClinVar as [Benign]. Clinvar id is 3038017.Status of the report is no_assertion_criteria_provided, 0 stars.

BS2

High AC in GnomAd4 at 824 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ATF3	NM_001674.4 linkuse as main transcript	c.*6C>T		3_prime_UTR_variant	4/4	ENST00000341491.9	NP_001665.1	P18847-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ATF3	ENST00000341491.9 linkuse as main transcript	c.*6C>T		3_prime_UTR_variant	4/4	1	NM_001674.4	ENSP00000344352.4		P18847-1

Frequencies

GnomAD3 genomes

AF:

0.00542

AC:

824

AN:

152136

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00113

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00308

Gnomad ASJ

AF:

0.0118

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.0106

Gnomad FIN

AF:

0.00765

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.00808

Gnomad OTH

AF:

0.00239

GnomAD3 exomes

AF:

0.00653

AC:

1641

AN:

251110

Hom.:

AF XY:

0.00706

AC XY:

958

AN XY:

135756

show subpopulations

Gnomad AFR exome

AF:

0.00111

Gnomad AMR exome

AF:

0.00310

Gnomad ASJ exome

AF:

0.0109

Gnomad EAS exome

AF:

0.000109

Gnomad SAS exome

AF:

0.0123

Gnomad FIN exome

AF:

0.00855

Gnomad NFE exome

AF:

0.00701

Gnomad OTH exome

AF:

0.00768

GnomAD4 exome

AF:

0.00698

AC:

10207

AN:

1461586

Hom.:

Cov.:

AF XY:

0.00724

AC XY:

5263

AN XY:

727084

show subpopulations

Gnomad4 AFR exome

AF:

0.000986

Gnomad4 AMR exome

AF:

0.00353

Gnomad4 ASJ exome

AF:

0.00999

Gnomad4 EAS exome

AF:

0.0000252

Gnomad4 SAS exome

AF:

0.0111

Gnomad4 FIN exome

AF:

0.00801

Gnomad4 NFE exome

AF:

0.00713

Gnomad4 OTH exome

AF:

0.00646

GnomAD4 genome

AF:

0.00541

AC:

824

AN:

152254

Hom.:

Cov.:

AF XY:

0.00563

AC XY:

419

AN XY:

74440

show subpopulations

Gnomad4 AFR

AF:

0.00113

Gnomad4 AMR

AF:

0.00307

Gnomad4 ASJ

AF:

0.0118

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.0106

Gnomad4 FIN

AF:

0.00765

Gnomad4 NFE

AF:

0.00809

Gnomad4 OTH

AF:

0.00236

Alfa

AF:

0.00640

Hom.:

Bravo

AF:

0.00451

Asia WGS

AF:

0.00346

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

ATF3-related disorder

Benign:1

Benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

May 07, 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

-0.83

CADD

Benign

0.23

DANN

Benign

0.63

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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