19-55745893-C-T

Variant names:

• chr19-55745893-C-T
• rs2194

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 0.249 in 152,010 control chromosomes in the GnomAD database, including 4,986 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 0.25 (4986 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.42

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.31 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: 0.249 AC: 37765 AN: 151892 Hom.: 4990 Cov.: 32

Gnomad AFR AF: 0.202

Gnomad AMI AF: 0.246

Gnomad AMR AF: 0.198

Gnomad ASJ AF: 0.232

Gnomad EAS AF: 0.0559

Gnomad SAS AF: 0.177

Gnomad FIN AF: 0.225

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.313

Gnomad OTH AF: 0.241

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

GnomAD4 genome AF: 0.249 AC: 37776 AN: 152010 Hom.: 4986 Cov.: 32 AF XY: 0.240 AC XY: 17795 AN XY: 74296

Gnomad4 AFR AF: 0.202

Gnomad4 AMR AF: 0.197

Gnomad4 ASJ AF: 0.232

Gnomad4 EAS AF: 0.0560

Gnomad4 SAS AF: 0.177

Gnomad4 FIN AF: 0.225

Gnomad4 NFE AF: 0.313

Gnomad4 OTH AF: 0.239

Alfa AF: 0.295 Hom.: 14277

Bravo AF: 0.245

Asia WGS AF: 0.119 AC: 414 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.20
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2194; hg19: chr19-56257259;