dbSNP rs10475: ATF3:c.*716T>C (chr1-212620271-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001674.4(ATF3):c.*716T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.754 in 153,034 control chromosomes in the GnomAD database, including 43,965 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.75 ( 43683 hom., cov: 32)

Exomes 𝑓: 0.79 ( 282 hom. )

Consequence

ATF3
NM_001674.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0360

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:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.78 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ATF3	NM_001674.4 link	c.*716T>C		3_prime_UTR_variant	Exon 4 of 4	ENST00000341491.9	NP_001665.1	P18847-1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
ATF3	ENST00000341491.9 link	c.*716T>C	3_prime_UTR_variant	Exon 4 of 4	1	NM_001674.4	ENSP00000344352.4	P18847-1
ATF3	ENST00000366987.6 link	c.*716T>C	3_prime_UTR_variant	Exon 4 of 4	1		ENSP00000355954.2	P18847-1
ATF3	ENST00000492118.2 link	n.1597T>C	non_coding_transcript_exon_variant	Exon 2 of 2	2

Frequencies

GnomAD3 genomes

AF:

0.754

AC:

114606

AN:

152026

Hom.:

43652

Cov.:

show subpopulations

Gnomad AFR

AF:

0.738

Gnomad AMI

AF:

0.905

Gnomad AMR

AF:

0.747

Gnomad ASJ

AF:

0.737

Gnomad EAS

AF:

0.427

Gnomad SAS

AF:

0.701

Gnomad FIN

AF:

0.801

Gnomad MID

AF:

0.788

Gnomad NFE

AF:

0.786

Gnomad OTH

AF:

0.736

GnomAD4 exome

AF:

0.789

AC:

702

AN:

890

Hom.:

282

Cov.:

AF XY:

0.798

AC XY:

404

AN XY:

506

show subpopulations

Gnomad4 AFR exome

AF:

1.00

AC:

AN:

Gnomad4 AMR exome

AF:

0.722

AC:

AN:

Gnomad4 ASJ exome

AC:

AN:

Gnomad4 EAS exome

AC:

AN:

Gnomad4 SAS exome

AF:

0.857

AC:

AN:

Gnomad4 FIN exome

AF:

0.798

AC:

340

AN:

426

Gnomad4 NFE exome

AF:

0.786

AC:

313

AN:

398

Gnomad4 Remaining exome

AF:

0.643

AC:

AN:

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Exome Het

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.754

AC:

114699

AN:

152144

Hom.:

43683

Cov.:

AF XY:

0.750

AC XY:

55810

AN XY:

74402

show subpopulations

Gnomad4 AFR

AF:

0.738

AC:

0.73838

AN:

0.73838

Gnomad4 AMR

AF:

0.747

AC:

0.7465

AN:

0.7465

Gnomad4 ASJ

AF:

0.737

AC:

0.737313

AN:

0.737313

Gnomad4 EAS

AF:

0.427

AC:

0.426801

AN:

0.426801

Gnomad4 SAS

AF:

0.700

AC:

0.699793

AN:

0.699793

Gnomad4 FIN

AF:

0.801

AC:

0.800906

AN:

0.800906

Gnomad4 NFE

AF:

0.786

AC:

0.785508

AN:

0.785508

Gnomad4 OTH

AF:

0.738

AC:

0.737689

AN:

0.737689

Heterozygous variant carriers

1443

2885

4328

5770

7213

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Genome Het

Genome Hom

Variant carriers

848

1696

2544

3392

4240

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.769

Hom.:

169468

Bravo

AF:

0.748

Asia WGS

AF:

0.628

AC:

2188

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

3.4

DANN

Benign

0.56

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

Mutation Taster

=100/0

polymorphism (auto)

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over