rs4802981

chr19-52692173-C-Gchr19-52692173-C-T

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 0.725 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.885

Gnomad4 AMR AF: 0.660

Gnomad4 ASJ AF: 0.630

Gnomad4 EAS AF: 0.581

Gnomad4 SAS AF: 0.541

Gnomad4 FIN AF: 0.664

Gnomad4 NFE AF: 0.681

Gnomad4 OTH AF: 0.702

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4802981; hg19: chr19-53195426;