rs12745240

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr1-161758211-G-A
• chr1-161758211-G-C
• chr1-161758211-G-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000702792.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ATF6-DT	ENST00000702792.1		n.372+7217C>T		intron	N/A
	ATF6-DT	ENST00000792236.1		n.548-1344C>T		intron	N/A

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

African (AFR) AF: 0.399 AC: 16288 AN: 40786

American (AMR) AF: 0.317 AC: 4771 AN: 15048

Ashkenazi Jewish (ASJ) AF: 0.343 AC: 1184 AN: 3456

East Asian (EAS) AF: 0.480 AC: 2432 AN: 5068

South Asian (SAS) AF: 0.384 AC: 1832 AN: 4768

European-Finnish (FIN) AF: 0.324 AC: 3214 AN: 9922

Middle Eastern (MID) AF: 0.413 AC: 119 AN: 288

European-Non Finnish (NFE) AF: 0.388 AC: 26279 AN: 67702

Other (OTH) AF: 0.385 AC: 804 AN: 2088

Alfa AF: 0.380 Hom.: 5756

Bravo AF: 0.382

Asia WGS AF: 0.418 AC: 1446 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.54
DANN	Benign	0.37
PhyloP100		-0.99

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs12745240;

hg19: chr1-161728001;