chr19-50902552-C-T

Variant names:

• chr19-50902552-C-T
• rs806020

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 0.492 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.573 AC: 23684 AN: 41354

American (AMR) AF: 0.491 AC: 7490 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.564 AC: 1954 AN: 3466

East Asian (EAS) AF: 0.0516 AC: 266 AN: 5154

South Asian (SAS) AF: 0.318 AC: 1528 AN: 4810

European-Finnish (FIN) AF: 0.508 AC: 5346 AN: 10530

Middle Eastern (MID) AF: 0.497 AC: 146 AN: 294

European-Non Finnish (NFE) AF: 0.483 AC: 32832 AN: 67934

Other (OTH) AF: 0.484 AC: 1023 AN: 2112

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
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs806020; hg19: chr19-51405808;