14-86463582-T-C

Variant names:

• chr14-86463582-T-C
• rs2022771

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 0.373 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
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.198 AC: 8208 AN: 41496

American (AMR) AF: 0.352 AC: 5377 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.505 AC: 1752 AN: 3470

East Asian (EAS) AF: 0.535 AC: 2755 AN: 5148

South Asian (SAS) AF: 0.525 AC: 2529 AN: 4818

European-Finnish (FIN) AF: 0.428 AC: 4513 AN: 10552

Middle Eastern (MID) AF: 0.388 AC: 114 AN: 294

European-Non Finnish (NFE) AF: 0.447 AC: 30349 AN: 67962

Other (OTH) AF: 0.382 AC: 804 AN: 2106

Alfa AF: 0.422 Hom.: 43530

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
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs2022771; hg19: chr14-86929926;