rs3093211

Variant names:

• chr19-15877157-G-A
• rs3093211

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 0.288 in 151,732 control chromosomes in the GnomAD database, including 6,835 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 0.29 (6835 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.92

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.391 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: 0.288 AC: 43600 AN: 151614 Hom.: 6827 Cov.: 29

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.266

Gnomad AMR AF: 0.304

Gnomad ASJ AF: 0.388

Gnomad EAS AF: 0.244

Gnomad SAS AF: 0.406

Gnomad FIN AF: 0.296

Gnomad MID AF: 0.452

Gnomad NFE AF: 0.347

Gnomad OTH AF: 0.343

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

GnomAD4 genome AF: 0.288 AC: 43635 AN: 151732 Hom.: 6835 Cov.: 29 AF XY: 0.287 AC XY: 21295 AN XY: 74112

Gnomad4 AFR AF: 0.162

Gnomad4 AMR AF: 0.304

Gnomad4 ASJ AF: 0.388

Gnomad4 EAS AF: 0.245

Gnomad4 SAS AF: 0.406

Gnomad4 FIN AF: 0.296

Gnomad4 NFE AF: 0.347

Gnomad4 OTH AF: 0.346

Alfa AF: 0.314 Hom.: 956

Bravo AF: 0.281

Asia WGS AF: 0.345 AC: 1197 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.11
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3093211; hg19: chr19-15987967;