ENST00000366987.6:c.-4-23516C>T

Variant names:

• chr1-212591502-C-T
• rs11119982
• ENST00000366987.6:c.-4-23516C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000366987.6(ATF3):​c.-4-23516C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.401 in 151,994 control chromosomes in the GnomAD database, including 13,764 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 0.40 (13764 hom., cov: 31)
• Consequence: ATF3 ENST00000366987.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.36
• Publications: 10 publications found

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]

ACMG classification

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 = 0.491 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ATF3	NM_001030287.4	c.-4-23516C>T		intron_variant	Intron 1 of 3		NP_001025458.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ATF3	ENST00000366987.6	c.-4-23516C>T		intron_variant	Intron 1 of 3	1		ENSP00000355954.2
ATF3	ENST00000366981.8	c.-4-23516C>T		intron_variant	Intron 1 of 3	1		ENSP00000355948.4

Frequencies

GnomAD3 genomes AF: 0.401 AC: 60907 AN: 151876 Hom.: 13766 Cov.: 31

Gnomad AFR AF: 0.233

Gnomad AMI AF: 0.653

Gnomad AMR AF: 0.313

Gnomad ASJ AF: 0.490

Gnomad EAS AF: 0.177

Gnomad SAS AF: 0.455

Gnomad FIN AF: 0.607

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.496

Gnomad OTH AF: 0.418

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.401 AC: 60929 AN: 151994 Hom.: 13764 Cov.: 31 AF XY: 0.403 AC XY: 29915 AN XY: 74314

African (AFR) AF: 0.233 AC: 9647 AN: 41454

American (AMR) AF: 0.313 AC: 4783 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.490 AC: 1701 AN: 3470

East Asian (EAS) AF: 0.177 AC: 914 AN: 5162

South Asian (SAS) AF: 0.454 AC: 2190 AN: 4822

European-Finnish (FIN) AF: 0.607 AC: 6407 AN: 10552

Middle Eastern (MID) AF: 0.449 AC: 132 AN: 294

European-Non Finnish (NFE) AF: 0.496 AC: 33674 AN: 67928

Other (OTH) AF: 0.421 AC: 889 AN: 2112

Alfa AF: 0.461 Hom.: 70545

Bravo AF: 0.369

Asia WGS AF: 0.370 AC: 1281 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	0.0090
DANN	Benign	0.72
PhyloP100		-1.4
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

Other links and lift over

dbSNP: rs11119982; hg19: chr1-212764844;