rs3820449

chr1-161757382-G-Achr1-161757382-G-T

Variant summary

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

The ENST00000702792.1(ATF6-DT):n.373-7015C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.196 in 152,020 control chromosomes in the GnomAD database, including 3,670 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 0.20 (3659 hom., cov: 32)
  • Exomes 𝑓: 0.19 (11 hom.)
• Consequence: ATF6-DT ENST00000702792.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0610

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=-0.58).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.272 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ATF6-DT	ENST00000702792.1	n.373-7015C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.196 AC: 29682 AN: 151552 Hom.: 3661 Cov.: 32

Gnomad AFR AF: 0.0491

Gnomad AMI AF: 0.294

Gnomad AMR AF: 0.186

Gnomad ASJ AF: 0.229

Gnomad EAS AF: 0.284

Gnomad SAS AF: 0.182

Gnomad FIN AF: 0.272

Gnomad MID AF: 0.242

Gnomad NFE AF: 0.267

Gnomad OTH AF: 0.199

GnomAD4 exome AF: 0.189 AC: 66 AN: 350 Hom.: 11 AF XY: 0.165 AC XY: 30 AN XY: 182

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.100

Gnomad4 ASJ exome AF: 0.167

Gnomad4 EAS exome AF: 0.500

Gnomad4 SAS exome AF: 0.118

Gnomad4 FIN exome AF: 0.100

Gnomad4 NFE exome AF: 0.219

Gnomad4 OTH exome AF: 0.214

GnomAD4 genome AF: 0.196 AC: 29680 AN: 151670 Hom.: 3659 Cov.: 32 AF XY: 0.196 AC XY: 14494 AN XY: 74104

Gnomad4 AFR AF: 0.0492

Gnomad4 AMR AF: 0.186

Gnomad4 ASJ AF: 0.229

Gnomad4 EAS AF: 0.284

Gnomad4 SAS AF: 0.182

Gnomad4 FIN AF: 0.272

Gnomad4 NFE AF: 0.267

Gnomad4 OTH AF: 0.197

Alfa AF: 0.223 Hom.: 1502

Bravo AF: 0.183

Asia WGS AF: 0.200 AC: 689 AN: 3452

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.58
Cadd	Benign	8.2
Dann	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3820449; hg19: chr1-161727172;