rs11571530

Variant names:

• chr1-212612072-G-T
• rs11571530
• NM_001674.4:c.-4-2946G>T

Variant summary

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

The NM_001674.4(ATF3):​c.-4-2946G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.042 in 152,234 control chromosomes in the GnomAD database, including 475 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 0.042 (475 hom., cov: 33)
• Consequence: ATF3 NM_001674.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0580
• Publications: 1 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=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.2 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ATF3	NM_001674.4	c.-4-2946G>T		intron_variant	Intron 1 of 3	ENST00000341491.9	NP_001665.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ATF3	ENST00000341491.9	c.-4-2946G>T		intron_variant	Intron 1 of 3	1	NM_001674.4	ENSP00000344352.4

Frequencies

GnomAD3 genomes AF: 0.0420 AC: 6392 AN: 152116 Hom.: 472 Cov.: 33

Gnomad AFR AF: 0.00818

Gnomad AMI AF: 0.00658

Gnomad AMR AF: 0.205

Gnomad ASJ AF: 0.0101

Gnomad EAS AF: 0.131

Gnomad SAS AF: 0.0180

Gnomad FIN AF: 0.0300

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0248

Gnomad OTH AF: 0.0509

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

GnomAD4 genome AF: 0.0420 AC: 6401 AN: 152234 Hom.: 475 Cov.: 33 AF XY: 0.0458 AC XY: 3405 AN XY: 74426

African (AFR) AF: 0.00816 AC: 339 AN: 41550

American (AMR) AF: 0.205 AC: 3140 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0101 AC: 35 AN: 3472

East Asian (EAS) AF: 0.131 AC: 680 AN: 5190

South Asian (SAS) AF: 0.0180 AC: 87 AN: 4828

European-Finnish (FIN) AF: 0.0300 AC: 318 AN: 10592

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.0248 AC: 1687 AN: 68012

Other (OTH) AF: 0.0509 AC: 107 AN: 2104

Alfa AF: 0.0301 Hom.: 48

Bravo AF: 0.0589

Asia WGS AF: 0.0720 AC: 248 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.3
DANN	Benign	0.74
PhyloP100		-0.058
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: rs11571530; hg19: chr1-212785414;