rs799032

Variant names:

• chr14-82171001-G-A
• rs799032

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 0.478 in 151,806 control chromosomes in the GnomAD database, including 17,945 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 0.48 (17945 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.502

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.544 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: 0.478 AC: 72466 AN: 151688 Hom.: 17934 Cov.: 32

Gnomad AFR AF: 0.387

Gnomad AMI AF: 0.658

Gnomad AMR AF: 0.411

Gnomad ASJ AF: 0.456

Gnomad EAS AF: 0.389

Gnomad SAS AF: 0.389

Gnomad FIN AF: 0.552

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.548

Gnomad OTH AF: 0.491

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

GnomAD4 genome AF: 0.478 AC: 72529 AN: 151806 Hom.: 17945 Cov.: 32 AF XY: 0.474 AC XY: 35198 AN XY: 74216

Gnomad4 AFR AF: 0.387

Gnomad4 AMR AF: 0.410

Gnomad4 ASJ AF: 0.456

Gnomad4 EAS AF: 0.389

Gnomad4 SAS AF: 0.390

Gnomad4 FIN AF: 0.552

Gnomad4 NFE AF: 0.548

Gnomad4 OTH AF: 0.495

Alfa AF: 0.531 Hom.: 34967

Bravo AF: 0.462

Asia WGS AF: 0.403 AC: 1398 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	6.3
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs799032; hg19: chr14-82637345;