rs2022771

chr14-86463582-T-Cchr14-86463582-T-G

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 0.373 in 152,032 control chromosomes in the GnomAD database, including 11,688 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 0.37 (11688 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.278

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.518 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: 0.373 AC: 56703 AN: 151916 Hom.: 11672 Cov.: 32

Gnomad AFR AF: 0.198

Gnomad AMI AF: 0.377

Gnomad AMR AF: 0.352

Gnomad ASJ AF: 0.505

Gnomad EAS AF: 0.534

Gnomad SAS AF: 0.526

Gnomad FIN AF: 0.428

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.447

Gnomad OTH AF: 0.376

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

GnomAD4 genome AF: 0.373 AC: 56744 AN: 152032 Hom.: 11688 Cov.: 32 AF XY: 0.374 AC XY: 27771 AN XY: 74310

Gnomad4 AFR AF: 0.198

Gnomad4 AMR AF: 0.352

Gnomad4 ASJ AF: 0.505

Gnomad4 EAS AF: 0.535

Gnomad4 SAS AF: 0.525

Gnomad4 FIN AF: 0.428

Gnomad4 NFE AF: 0.447

Gnomad4 OTH AF: 0.382

Alfa AF: 0.433 Hom.: 19713

Bravo AF: 0.359

Asia WGS AF: 0.516 AC: 1793 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
Cadd	Benign	7.7
Dann	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2022771; hg19: chr14-86929926;