rs1782159

Variant names:

• chr14-41287366-C-T
• rs1782159

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.822

Gnomad4 AMR AF: 0.785

Gnomad4 ASJ AF: 0.771

Gnomad4 EAS AF: 0.751

Gnomad4 SAS AF: 0.656

Gnomad4 FIN AF: 0.684

Gnomad4 NFE AF: 0.728

Gnomad4 OTH AF: 0.776

Alfa AF: 0.755 Hom.: 5404

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1782159; hg19: chr14-41756569;