rs1782159

Positions:

• chr14-41287366-C-T

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;