rs799032

Variant names:

• chr14-82171001-G-A
• rs799032

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 0.478 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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.387 AC: 16031 AN: 41432

American (AMR) AF: 0.410 AC: 6251 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.456 AC: 1583 AN: 3472

East Asian (EAS) AF: 0.389 AC: 2004 AN: 5152

South Asian (SAS) AF: 0.390 AC: 1880 AN: 4824

European-Finnish (FIN) AF: 0.552 AC: 5822 AN: 10540

Middle Eastern (MID) AF: 0.408 AC: 120 AN: 294

European-Non Finnish (NFE) AF: 0.548 AC: 37197 AN: 67848

Other (OTH) AF: 0.495 AC: 1042 AN: 2104

Alfa AF: 0.517 Hom.: 56322

Bravo AF: 0.462

Asia WGS AF: 0.403 AC: 1398 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	6.3
DANN	Benign	0.67
PhyloP100		0.50

Splicing

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

Other links and lift over

dbSNP: rs799032; hg19: chr14-82637345;