chr19-50902417-T-C

Position:

• chr19-50902417-T-C

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 0.39 in 151,834 control chromosomes in the GnomAD database, including 12,806 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 0.39 (12806 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.59

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.474 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.391 AC: 59269 AN: 151716 Hom.: 12812 Cov.: 30

Gnomad AFR AF: 0.243

Gnomad AMI AF: 0.519

Gnomad AMR AF: 0.442

Gnomad ASJ AF: 0.519

Gnomad EAS AF: 0.0323

Gnomad SAS AF: 0.266

Gnomad FIN AF: 0.506

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.479

Gnomad OTH AF: 0.412

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

GnomAD4 genome AF: 0.390 AC: 59287 AN: 151834 Hom.: 12806 Cov.: 30 AF XY: 0.390 AC XY: 28915 AN XY: 74184

Gnomad4 AFR AF: 0.242

Gnomad4 AMR AF: 0.442

Gnomad4 ASJ AF: 0.519

Gnomad4 EAS AF: 0.0328

Gnomad4 SAS AF: 0.266

Gnomad4 FIN AF: 0.506

Gnomad4 NFE AF: 0.479

Gnomad4 OTH AF: 0.407

Alfa AF: 0.421 Hom.: 2823

Bravo AF: 0.381

Asia WGS AF: 0.152 AC: 533 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.58
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs806021; hg19: chr19-51405673;