rs6691852

Variant names:

• chr1-212597080-T-C
• rs6691852
• ENST00000366987.6:c.-4-17938T>C

Variant summary

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

The ENST00000366987.6(ATF3):​c.-4-17938T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.872 in 152,232 control chromosomes in the GnomAD database, including 58,411 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 0.87 (58411 hom., cov: 31)
• Consequence: ATF3 ENST00000366987.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.468
• Publications: 4 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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.922 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000366987.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ATF3	NM_001030287.4		c.-4-17938T>C		intron	N/A	NP_001025458.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ATF3	ENST00000366987.6	TSL:1	c.-4-17938T>C		intron	N/A	ENSP00000355954.2
	ATF3	ENST00000366981.8	TSL:1	c.-4-17938T>C		intron	N/A	ENSP00000355948.4

Frequencies

GnomAD3 genomes AF: 0.872 AC: 132697 AN: 152114 Hom.: 58383 Cov.: 31

Gnomad AFR AF: 0.816

Gnomad AMI AF: 0.940

Gnomad AMR AF: 0.746

Gnomad ASJ AF: 0.947

Gnomad EAS AF: 0.709

Gnomad SAS AF: 0.925

Gnomad FIN AF: 0.937

Gnomad MID AF: 0.946

Gnomad NFE AF: 0.928

Gnomad OTH AF: 0.887

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

GnomAD4 genome AF: 0.872 AC: 132778 AN: 152232 Hom.: 58411 Cov.: 31 AF XY: 0.870 AC XY: 64735 AN XY: 74434

African (AFR) AF: 0.816 AC: 33861 AN: 41516

American (AMR) AF: 0.745 AC: 11386 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.947 AC: 3288 AN: 3472

East Asian (EAS) AF: 0.709 AC: 3676 AN: 5182

South Asian (SAS) AF: 0.926 AC: 4467 AN: 4826

European-Finnish (FIN) AF: 0.937 AC: 9950 AN: 10618

Middle Eastern (MID) AF: 0.956 AC: 281 AN: 294

European-Non Finnish (NFE) AF: 0.928 AC: 63136 AN: 68024

Other (OTH) AF: 0.887 AC: 1876 AN: 2114

Alfa AF: 0.885 Hom.: 49812

Bravo AF: 0.850

Asia WGS AF: 0.844 AC: 2935 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.5
DANN	Benign	0.71
PhyloP100		-0.47
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: rs6691852; hg19: chr1-212770422;