rs12121310

chr1-161749425-A-Cchr1-161749425-A-G

Variant summary

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

The 1-161749425-A-C variant causes a downstream gene 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 ENST00000702792.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.551

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=-0.94).
• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ATF6-DT	ENST00000702792.1			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

Gnomad4 AFR AF: 0.384

Gnomad4 AMR AF: 0.293

Gnomad4 ASJ AF: 0.325

Gnomad4 EAS AF: 0.387

Gnomad4 SAS AF: 0.358

Gnomad4 FIN AF: 0.304

Gnomad4 NFE AF: 0.329

Gnomad4 OTH AF: 0.338

Alfa AF: 0.332 Hom.: 8103

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12121310; hg19: chr1-161719215;