rs799032

Positions:

• chr14-82171001-G-A

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/exons	MANE	UniProt

Ensembl

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