rs3093091

chr19-15898323-G-A

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 0.181 in 151,938 control chromosomes in the GnomAD database, including 2,548 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 0.18 (2548 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.26 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.181 AC: 27539 AN: 151820 Hom.: 2549 Cov.: 31

Gnomad AFR AF: 0.190

Gnomad AMI AF: 0.141

Gnomad AMR AF: 0.154

Gnomad ASJ AF: 0.194

Gnomad EAS AF: 0.160

Gnomad SAS AF: 0.273

Gnomad FIN AF: 0.166

Gnomad MID AF: 0.287

Gnomad NFE AF: 0.179

Gnomad OTH AF: 0.177

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

GnomAD4 genome AF: 0.181 AC: 27555 AN: 151938 Hom.: 2548 Cov.: 31 AF XY: 0.180 AC XY: 13386 AN XY: 74240

Gnomad4 AFR AF: 0.190

Gnomad4 AMR AF: 0.154

Gnomad4 ASJ AF: 0.194

Gnomad4 EAS AF: 0.160

Gnomad4 SAS AF: 0.272

Gnomad4 FIN AF: 0.166

Gnomad4 NFE AF: 0.179

Gnomad4 OTH AF: 0.178

Alfa AF: 0.176 Hom.: 289

Bravo AF: 0.181

Asia WGS AF: 0.214 AC: 746 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
Cadd	Benign	2.8
Dann	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3093091; hg19: chr19-16009133;