19-50914702-C-T

Variant names:

• chr19-50914702-C-T
• rs7246794

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 0.0744 in 152,230 control chromosomes in the GnomAD database, including 639 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 0.074 (639 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.13
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.161 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: 0.0743 AC: 11301 AN: 152112 Hom.: 635 Cov.: 32

Gnomad AFR AF: 0.164

Gnomad AMI AF: 0.00548

Gnomad AMR AF: 0.0420

Gnomad ASJ AF: 0.0158

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0441

Gnomad FIN AF: 0.0301

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0460

Gnomad OTH AF: 0.0555

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

GnomAD4 genome AF: 0.0744 AC: 11324 AN: 152230 Hom.: 639 Cov.: 32 AF XY: 0.0724 AC XY: 5387 AN XY: 74424

African (AFR) AF: 0.165 AC: 6834 AN: 41522

American (AMR) AF: 0.0421 AC: 643 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0158 AC: 55 AN: 3472

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5188

South Asian (SAS) AF: 0.0435 AC: 210 AN: 4828

European-Finnish (FIN) AF: 0.0301 AC: 319 AN: 10604

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0460 AC: 3128 AN: 68010

Other (OTH) AF: 0.0554 AC: 117 AN: 2112

Alfa AF: 0.0442 Hom.: 67

Bravo AF: 0.0790

Asia WGS AF: 0.0270 AC: 92 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.7
DANN	Benign	0.41
PhyloP100		2.1

Splicing

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

Other links and lift over

dbSNP: rs7246794; hg19: chr19-51417958;