19-50920290-C-T

Variant names:

• chr19-50920290-C-T
• rs8100631

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 0.405 in 152,050 control chromosomes in the GnomAD database, including 13,085 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 0.40 (13085 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.971
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.8 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: 0.405 AC: 61516 AN: 151932 Hom.: 13081 Cov.: 32

Gnomad AFR AF: 0.429

Gnomad AMI AF: 0.429

Gnomad AMR AF: 0.328

Gnomad ASJ AF: 0.337

Gnomad EAS AF: 0.821

Gnomad SAS AF: 0.536

Gnomad FIN AF: 0.349

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.378

Gnomad OTH AF: 0.403

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

GnomAD4 genome AF: 0.405 AC: 61551 AN: 152050 Hom.: 13085 Cov.: 32 AF XY: 0.404 AC XY: 30053 AN XY: 74334

African (AFR) AF: 0.429 AC: 17807 AN: 41464

American (AMR) AF: 0.328 AC: 5019 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.337 AC: 1167 AN: 3468

East Asian (EAS) AF: 0.821 AC: 4241 AN: 5166

South Asian (SAS) AF: 0.536 AC: 2588 AN: 4830

European-Finnish (FIN) AF: 0.349 AC: 3682 AN: 10556

Middle Eastern (MID) AF: 0.401 AC: 118 AN: 294

European-Non Finnish (NFE) AF: 0.378 AC: 25691 AN: 67966

Other (OTH) AF: 0.401 AC: 847 AN: 2110

Alfa AF: 0.388 Hom.: 50154

Bravo AF: 0.404

Asia WGS AF: 0.640 AC: 2221 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.6
DANN	Benign	0.66
PhyloP100		0.97

Splicing

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

Other links and lift over

dbSNP: rs8100631; hg19: chr19-51423546;