rs4804803

Positions:

• chr19-7747847-A-G

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

protective, no assertion criteria provided

literature only

OMIM

Feb 01, 2006

- -

Mycobacterium tuberculosis, susceptibility to Other:1

risk factor, no assertion criteria provided

literature only

OMIM

Feb 01, 2006

- -

Susceptibility to HIV infection Other:1

risk factor, no assertion criteria provided

literature only

OMIM

Feb 01, 2006

- -

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;