ENST00000702792.1:n.372+7217C>T

Variant names:

• chr1-161758211-G-A
• rs12745240
• ENST00000702792.1:n.372+7217C>T

Variant summary

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

The ENST00000702792.1(ATF6-DT):​n.372+7217C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.382 in 150,028 control chromosomes in the GnomAD database, including 11,007 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 0.38 (11007 hom., cov: 28)
• Consequence: ATF6-DT ENST00000702792.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.987

Genes affected

ATF6-DT (HGNC:55826): (ATF6 divergent transcript)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.464 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ATF6-DT	ENST00000702792.1	n.372+7217C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.382 AC: 57254 AN: 149966 Hom.: 11004 Cov.: 28

Gnomad AFR AF: 0.399

Gnomad AMI AF: 0.391

Gnomad AMR AF: 0.317

Gnomad ASJ AF: 0.343

Gnomad EAS AF: 0.480

Gnomad SAS AF: 0.385

Gnomad FIN AF: 0.324

Gnomad MID AF: 0.410

Gnomad NFE AF: 0.388

Gnomad OTH AF: 0.386

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

GnomAD4 genome AF: 0.382 AC: 57276 AN: 150028 Hom.: 11007 Cov.: 28 AF XY: 0.379 AC XY: 27694 AN XY: 73118

Gnomad4 AFR AF: 0.399

Gnomad4 AMR AF: 0.317

Gnomad4 ASJ AF: 0.343

Gnomad4 EAS AF: 0.480

Gnomad4 SAS AF: 0.384

Gnomad4 FIN AF: 0.324

Gnomad4 NFE AF: 0.388

Gnomad4 OTH AF: 0.385

Alfa AF: 0.378 Hom.: 5101

Bravo AF: 0.382

Asia WGS AF: 0.418 AC: 1446 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.54
DANN	Benign	0.37

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs12745240; hg19: chr1-161728001;