rs4803596

Variant names:

• chr19-43301176-G-A
• rs4803596

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 0.0851 in 152,162 control chromosomes in the GnomAD database, including 725 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 0.085 (725 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.963

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.278 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: 0.0851 AC: 12942 AN: 152044 Hom.: 722 Cov.: 32

Gnomad AFR AF: 0.0823

Gnomad AMI AF: 0.118

Gnomad AMR AF: 0.121

Gnomad ASJ AF: 0.0862

Gnomad EAS AF: 0.289

Gnomad SAS AF: 0.0899

Gnomad FIN AF: 0.0554

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0668

Gnomad OTH AF: 0.0913

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

GnomAD4 genome AF: 0.0851 AC: 12951 AN: 152162 Hom.: 725 Cov.: 32 AF XY: 0.0859 AC XY: 6389 AN XY: 74388

Gnomad4 AFR AF: 0.0822

Gnomad4 AMR AF: 0.121

Gnomad4 ASJ AF: 0.0862

Gnomad4 EAS AF: 0.290

Gnomad4 SAS AF: 0.0898

Gnomad4 FIN AF: 0.0554

Gnomad4 NFE AF: 0.0667

Gnomad4 OTH AF: 0.0927

Alfa AF: 0.0749 Hom.: 484

Bravo AF: 0.0921

Asia WGS AF: 0.183 AC: 636 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.4
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4803596; hg19: chr19-43805328;