rs4802981

Variant names:

• chr19-52692173-C-G
• rs4802981

Your query was ambiguous. Multiple possible variants found:

• chr19-52692173-C-G
• chr19-52692173-C-T

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 0.725 in 152,132 control chromosomes in the GnomAD database, including 40,854 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 0.73 (40854 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.10
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.877 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: 0.725 AC: 110210 AN: 152014 Hom.: 40800 Cov.: 32

Gnomad AFR AF: 0.885

Gnomad AMI AF: 0.758

Gnomad AMR AF: 0.660

Gnomad ASJ AF: 0.630

Gnomad EAS AF: 0.580

Gnomad SAS AF: 0.541

Gnomad FIN AF: 0.664

Gnomad MID AF: 0.715

Gnomad NFE AF: 0.681

Gnomad OTH AF: 0.708

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

GnomAD4 genome AF: 0.725 AC: 110320 AN: 152132 Hom.: 40854 Cov.: 32 AF XY: 0.722 AC XY: 53667 AN XY: 74352

African (AFR) AF: 0.885 AC: 36759 AN: 41538

American (AMR) AF: 0.660 AC: 10089 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.630 AC: 2188 AN: 3472

East Asian (EAS) AF: 0.581 AC: 3000 AN: 5164

South Asian (SAS) AF: 0.541 AC: 2610 AN: 4822

European-Finnish (FIN) AF: 0.664 AC: 7010 AN: 10550

Middle Eastern (MID) AF: 0.724 AC: 213 AN: 294

European-Non Finnish (NFE) AF: 0.681 AC: 46277 AN: 67980

Other (OTH) AF: 0.702 AC: 1483 AN: 2114

Alfa AF: 0.713 Hom.: 4572

Bravo AF: 0.733

Asia WGS AF: 0.581 AC: 2019 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.49
DANN	Benign	0.26
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs4802981; hg19: chr19-53195426;