rs1782159

Variant names:

• chr14-41287366-C-T
• rs1782159

Variant summary

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

The variant allele was found at a frequency of 0.756 in 151,952 control chromosomes in the GnomAD database, including 43,676 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 0.76 (43676 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.948
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.814 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

Frequencies

GnomAD3 genomes AF: 0.756 AC: 114811 AN: 151834 Hom.: 43617 Cov.: 31

Gnomad AFR AF: 0.822

Gnomad AMI AF: 0.731

Gnomad AMR AF: 0.785

Gnomad ASJ AF: 0.771

Gnomad EAS AF: 0.750

Gnomad SAS AF: 0.656

Gnomad FIN AF: 0.684

Gnomad MID AF: 0.763

Gnomad NFE AF: 0.728

Gnomad OTH AF: 0.772

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

GnomAD4 genome AF: 0.756 AC: 114930 AN: 151952 Hom.: 43676 Cov.: 31 AF XY: 0.756 AC XY: 56102 AN XY: 74246

African (AFR) AF: 0.822 AC: 34069 AN: 41460

American (AMR) AF: 0.785 AC: 11970 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.771 AC: 2675 AN: 3470

East Asian (EAS) AF: 0.751 AC: 3867 AN: 5152

South Asian (SAS) AF: 0.656 AC: 3159 AN: 4818

European-Finnish (FIN) AF: 0.684 AC: 7222 AN: 10564

Middle Eastern (MID) AF: 0.762 AC: 224 AN: 294

European-Non Finnish (NFE) AF: 0.728 AC: 49445 AN: 67936

Other (OTH) AF: 0.776 AC: 1634 AN: 2106

Alfa AF: 0.757 Hom.: 5666

Bravo AF: 0.767

Asia WGS AF: 0.730 AC: 2534 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.20
DANN	Benign	0.29
PhyloP100		-0.95

Splicing

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

Other links and lift over

dbSNP: rs1782159; hg19: chr14-41756569;