rs4804803

Variant names:

• chr19-7747847-A-G
• rs4804803

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 0.253 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.253 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

Gnomad4 AFR AF: 0.412

Gnomad4 AMR AF: 0.180

Gnomad4 ASJ AF: 0.233

Gnomad4 EAS AF: 0.0702

Gnomad4 SAS AF: 0.191

Gnomad4 FIN AF: 0.200

Gnomad4 NFE AF: 0.198

Gnomad4 OTH AF: 0.234

Alfa AF: 0.213 Hom.: 3482

Bravo AF: 0.258

Asia WGS AF: 0.166 AC: 579 AN: 3478

ClinVar

Significance: protective; risk factor

Submissions summary: Benign:1 Other:2

Revision: no assertion criteria provided

Submissions by phenotype

Dengue fever, protection against Benign:1

Feb 01, 2006

OMIM

Significance: protective

Review Status: no assertion criteria provided

Collection Method: literature only

- -

Mycobacterium tuberculosis, susceptibility to Other:1

Feb 01, 2006

OMIM

Significance: risk factor

Review Status: no assertion criteria provided

Collection Method: literature only

- -

Susceptibility to HIV infection Other:1

Feb 01, 2006

OMIM

Significance: risk factor

Review Status: no assertion criteria provided

Collection Method: literature only

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.9
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: rs4804803; hg19: chr19-7812733;