chr1-161749425-A-C

Variant names:

• chr1-161749425-A-C
• rs12121310
• ENST00000792245.1:n.940T>G

Variant summary

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

The ENST00000792245.1(ATF6-DT):​n.940T>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.342 in 152,140 control chromosomes in the GnomAD database, including 9,026 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 0.34 (9026 hom., cov: 32)
• Consequence: ATF6-DT ENST00000792245.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.551
• Publications: 3 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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.379 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	ENST00000792245.1	n.940T>G		non_coding_transcript_exon_variant	Exon 1 of 1
ATF6-DT	ENST00000702792.1	n.*27T>G		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.342 AC: 51948 AN: 152022 Hom.: 9016 Cov.: 32

Gnomad AFR AF: 0.384

Gnomad AMI AF: 0.302

Gnomad AMR AF: 0.293

Gnomad ASJ AF: 0.325

Gnomad EAS AF: 0.387

Gnomad SAS AF: 0.358

Gnomad FIN AF: 0.304

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.329

Gnomad OTH AF: 0.341

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

GnomAD4 genome AF: 0.342 AC: 51986 AN: 152140 Hom.: 9026 Cov.: 32 AF XY: 0.341 AC XY: 25360 AN XY: 74362

African (AFR) AF: 0.384 AC: 15927 AN: 41484

American (AMR) AF: 0.293 AC: 4483 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.325 AC: 1127 AN: 3472

East Asian (EAS) AF: 0.387 AC: 2004 AN: 5174

South Asian (SAS) AF: 0.358 AC: 1728 AN: 4830

European-Finnish (FIN) AF: 0.304 AC: 3217 AN: 10572

Middle Eastern (MID) AF: 0.378 AC: 111 AN: 294

European-Non Finnish (NFE) AF: 0.329 AC: 22400 AN: 67996

Other (OTH) AF: 0.338 AC: 714 AN: 2110

Alfa AF: 0.333 Hom.: 10421

Bravo AF: 0.341

Asia WGS AF: 0.357 AC: 1239 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.60
DANN	Benign	0.40
PhyloP100		-0.55
PromoterAI		0.045	Neutral

Splicing

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

Other links and lift over

dbSNP: rs12121310; hg19: chr1-161719215;