rs4803759

Variant names:

• chr19-44824202-T-C
• rs4803759

Your query was ambiguous. Multiple possible variants found:

• chr19-44824202-T-C
• chr19-44824202-T-G

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 0.741 in 151,804 control chromosomes in the GnomAD database, including 41,739 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 0.74 (41739 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.16
• Publications: 17 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.798 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: 0.741 AC: 112326 AN: 151684 Hom.: 41704 Cov.: 30

Gnomad AFR AF: 0.805

Gnomad AMI AF: 0.714

Gnomad AMR AF: 0.795

Gnomad ASJ AF: 0.723

Gnomad EAS AF: 0.614

Gnomad SAS AF: 0.726

Gnomad FIN AF: 0.729

Gnomad MID AF: 0.801

Gnomad NFE AF: 0.703

Gnomad OTH AF: 0.727

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

GnomAD4 genome AF: 0.741 AC: 112415 AN: 151804 Hom.: 41739 Cov.: 30 AF XY: 0.744 AC XY: 55203 AN XY: 74196

African (AFR) AF: 0.805 AC: 33326 AN: 41388

American (AMR) AF: 0.795 AC: 12114 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.723 AC: 2503 AN: 3464

East Asian (EAS) AF: 0.615 AC: 3133 AN: 5094

South Asian (SAS) AF: 0.727 AC: 3495 AN: 4808

European-Finnish (FIN) AF: 0.729 AC: 7693 AN: 10550

Middle Eastern (MID) AF: 0.810 AC: 238 AN: 294

European-Non Finnish (NFE) AF: 0.703 AC: 47743 AN: 67956

Other (OTH) AF: 0.721 AC: 1520 AN: 2108

Alfa AF: 0.726 Hom.: 4989

Bravo AF: 0.751

Asia WGS AF: 0.636 AC: 2216 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.84
DANN	Benign	0.62
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs4803759; hg19: chr19-45327459;