19-50899426-C-T

Variant names:

• chr19-50899426-C-T
• rs1654513

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 0.714 in 152,150 control chromosomes in the GnomAD database, including 40,680 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 0.71 (40680 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.275
• Publications: 5 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 (AFR) allele frequency at 95% confidence interval = 0.889 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: 0.714 AC: 108593 AN: 152032 Hom.: 40629 Cov.: 32

Gnomad AFR AF: 0.897

Gnomad AMI AF: 0.837

Gnomad AMR AF: 0.606

Gnomad ASJ AF: 0.796

Gnomad EAS AF: 0.215

Gnomad SAS AF: 0.632

Gnomad FIN AF: 0.587

Gnomad MID AF: 0.839

Gnomad NFE AF: 0.684

Gnomad OTH AF: 0.747

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

GnomAD4 genome AF: 0.714 AC: 108697 AN: 152150 Hom.: 40680 Cov.: 32 AF XY: 0.705 AC XY: 52456 AN XY: 74368

African (AFR) AF: 0.897 AC: 37256 AN: 41534

American (AMR) AF: 0.605 AC: 9257 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.796 AC: 2760 AN: 3468

East Asian (EAS) AF: 0.216 AC: 1117 AN: 5172

South Asian (SAS) AF: 0.633 AC: 3046 AN: 4814

European-Finnish (FIN) AF: 0.587 AC: 6202 AN: 10574

Middle Eastern (MID) AF: 0.861 AC: 253 AN: 294

European-Non Finnish (NFE) AF: 0.684 AC: 46465 AN: 67978

Other (OTH) AF: 0.746 AC: 1578 AN: 2114

Alfa AF: 0.672 Hom.: 13108

Bravo AF: 0.723

Asia WGS AF: 0.466 AC: 1625 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	2.8
DANN	Benign	0.68
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs1654513; hg19: chr19-51402682;