rs4804803

Variant names:

• chr19-7747847-A-G
• rs4804803

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 0.253 in 152,040 control chromosomes in the GnomAD database, including 5,673 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as protective,risk factor (no stars).

• Frequency: Genomes: 𝑓 0.25 (5673 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: protective; risk factor no assertion criteria provided B:1 O:2
• Conservation: PhyloP100: 0.0700
• Publications: 125 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.407 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: 0.253 AC: 38427 AN: 151922 Hom.: 5678 Cov.: 32

Gnomad AFR AF: 0.413

Gnomad AMI AF: 0.406

Gnomad AMR AF: 0.180

Gnomad ASJ AF: 0.233

Gnomad EAS AF: 0.0702

Gnomad SAS AF: 0.192

Gnomad FIN AF: 0.200

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.198

Gnomad OTH AF: 0.236

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

GnomAD4 genome AF: 0.253 AC: 38427 AN: 152040 Hom.: 5673 Cov.: 32 AF XY: 0.250 AC XY: 18571 AN XY: 74336

African (AFR) AF: 0.412 AC: 17073 AN: 41422

American (AMR) AF: 0.180 AC: 2748 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.233 AC: 807 AN: 3466

East Asian (EAS) AF: 0.0702 AC: 364 AN: 5188

South Asian (SAS) AF: 0.191 AC: 924 AN: 4826

European-Finnish (FIN) AF: 0.200 AC: 2121 AN: 10584

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.198 AC: 13453 AN: 67956

Other (OTH) AF: 0.234 AC: 495 AN: 2114

Alfa AF: 0.230 Hom.: 6704

Bravo AF: 0.258

Asia WGS AF: 0.166 AC: 579 AN: 3478

ClinVar

ClinVar submissions

Significance: protective; risk factor

Revision: no assertion criteria provided

Pathogenic	VUS	Benign	Condition
-	-	-	Dengue fever, protection against (1)
-	-	-	Mycobacterium tuberculosis, susceptibility to (1)
-	-	-	Susceptibility to HIV infection (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.9
DANN	Benign	0.74
PhyloP100		0.070
PromoterAI		0.019	Neutral

Splicing

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

Other links and lift over

dbSNP: rs4804803; hg19: chr19-7812733;