rs11119982

Positions:

• chr1-212591502-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001030287.4(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 NM_001030287.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.36

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

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
ATF3	NM_001030287.4	c.-4-23516C>T		intron_variant			NP_001025458.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ATF3	ENST00000366987.6	c.-4-23516C>T		intron_variant		1		ENSP00000355954.2
ATF3	ENST00000366981.8	c.-4-23516C>T		intron_variant		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

Gnomad4 AFR AF: 0.233

Gnomad4 AMR AF: 0.313

Gnomad4 ASJ AF: 0.490

Gnomad4 EAS AF: 0.177

Gnomad4 SAS AF: 0.454

Gnomad4 FIN AF: 0.607

Gnomad4 NFE AF: 0.496

Gnomad4 OTH AF: 0.421

Alfa AF: 0.471 Hom.: 35283

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

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

Other links and lift over

dbSNP: rs11119982; hg19: chr1-212764844;