rs806020

Positions:

• chr19-50902552-C-T

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 0.492 in 151,806 control chromosomes in the GnomAD database, including 19,112 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 0.49 (19112 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45

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 = 0.567 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: 0.492 AC: 74680 AN: 151688 Hom.: 19094 Cov.: 30

Gnomad AFR AF: 0.573

Gnomad AMI AF: 0.521

Gnomad AMR AF: 0.491

Gnomad ASJ AF: 0.564

Gnomad EAS AF: 0.0511

Gnomad SAS AF: 0.319

Gnomad FIN AF: 0.508

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.483

Gnomad OTH AF: 0.489

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

GnomAD4 genome AF: 0.492 AC: 74742 AN: 151806 Hom.: 19112 Cov.: 30 AF XY: 0.490 AC XY: 36367 AN XY: 74194

Gnomad4 AFR AF: 0.573

Gnomad4 AMR AF: 0.491

Gnomad4 ASJ AF: 0.564

Gnomad4 EAS AF: 0.0516

Gnomad4 SAS AF: 0.318

Gnomad4 FIN AF: 0.508

Gnomad4 NFE AF: 0.483

Gnomad4 OTH AF: 0.484

Alfa AF: 0.495 Hom.: 3869

Bravo AF: 0.496

Asia WGS AF: 0.207 AC: 722 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.96
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs806020; hg19: chr19-51405808;