rs4803759

Positions:

• chr19-44824202-T-C
• chr19-44824202-T-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 0.741 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.805

Gnomad4 AMR AF: 0.795

Gnomad4 ASJ AF: 0.723

Gnomad4 EAS AF: 0.615

Gnomad4 SAS AF: 0.727

Gnomad4 FIN AF: 0.729

Gnomad4 NFE AF: 0.703

Gnomad4 OTH AF: 0.721

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4803759; hg19: chr19-45327459;