rs4802754

Positions:

• chr19-50854664-G-A

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 0.229 in 151,760 control chromosomes in the GnomAD database, including 4,767 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 0.23 (4767 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.333

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.339 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: 0.229 AC: 34750 AN: 151642 Hom.: 4761 Cov.: 30

Gnomad AFR AF: 0.0886

Gnomad AMI AF: 0.257

Gnomad AMR AF: 0.327

Gnomad ASJ AF: 0.232

Gnomad EAS AF: 0.354

Gnomad SAS AF: 0.166

Gnomad FIN AF: 0.348

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.269

Gnomad OTH AF: 0.216

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

GnomAD4 genome AF: 0.229 AC: 34769 AN: 151760 Hom.: 4767 Cov.: 30 AF XY: 0.231 AC XY: 17157 AN XY: 74144

Gnomad4 AFR AF: 0.0885

Gnomad4 AMR AF: 0.327

Gnomad4 ASJ AF: 0.232

Gnomad4 EAS AF: 0.353

Gnomad4 SAS AF: 0.166

Gnomad4 FIN AF: 0.348

Gnomad4 NFE AF: 0.269

Gnomad4 OTH AF: 0.223

Alfa AF: 0.272 Hom.: 1785

Bravo AF: 0.222

Asia WGS AF: 0.262 AC: 911 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.8
DANN	Benign	0.92

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4802754; hg19: chr19-51357920;