rs4803596

Variant names:

• chr19-43301176-G-A
• rs4803596

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 0.0851 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
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• 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

African (AFR) AF: 0.0822 AC: 3413 AN: 41520

American (AMR) AF: 0.121 AC: 1855 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0862 AC: 299 AN: 3468

East Asian (EAS) AF: 0.290 AC: 1495 AN: 5160

South Asian (SAS) AF: 0.0898 AC: 433 AN: 4824

European-Finnish (FIN) AF: 0.0554 AC: 587 AN: 10590

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.0667 AC: 4538 AN: 67988

Other (OTH) AF: 0.0927 AC: 196 AN: 2114

Alfa AF: 0.0766 Hom.: 681

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
PhyloP100		0.96

Splicing

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

Other links and lift over

dbSNP: rs4803596; hg19: chr19-43805328;