19-50902417-T-C

Variant names:

• chr19-50902417-T-C
• rs806021

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 0.39 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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	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

African (AFR) AF: 0.242 AC: 10029 AN: 41398

American (AMR) AF: 0.442 AC: 6739 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.519 AC: 1802 AN: 3470

East Asian (EAS) AF: 0.0328 AC: 170 AN: 5182

South Asian (SAS) AF: 0.266 AC: 1279 AN: 4800

European-Finnish (FIN) AF: 0.506 AC: 5309 AN: 10496

Middle Eastern (MID) AF: 0.425 AC: 125 AN: 294

European-Non Finnish (NFE) AF: 0.479 AC: 32509 AN: 67932

Other (OTH) AF: 0.407 AC: 853 AN: 2098

Alfa AF: 0.386 Hom.: 7592

Bravo AF: 0.381

Asia WGS AF: 0.152 AC: 533 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.58
DANN	Benign	0.29
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs806021; hg19: chr19-51405673;