rs3093216

Variant names:

• chr19-15876927-A-G
• rs3093216

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 0.288 in 152,020 control chromosomes in the GnomAD database, including 6,848 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 (6848 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.143
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.39 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.288 AC: 43677 AN: 151900 Hom.: 6840 Cov.: 31

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.268

Gnomad AMR AF: 0.304

Gnomad ASJ AF: 0.388

Gnomad EAS AF: 0.246

Gnomad SAS AF: 0.405

Gnomad FIN AF: 0.297

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.347

Gnomad OTH AF: 0.344

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

GnomAD4 genome AF: 0.288 AC: 43712 AN: 152020 Hom.: 6848 Cov.: 31 AF XY: 0.287 AC XY: 21340 AN XY: 74296

African (AFR) AF: 0.162 AC: 6707 AN: 41480

American (AMR) AF: 0.304 AC: 4642 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.388 AC: 1345 AN: 3466

East Asian (EAS) AF: 0.247 AC: 1273 AN: 5156

South Asian (SAS) AF: 0.405 AC: 1947 AN: 4808

European-Finnish (FIN) AF: 0.297 AC: 3139 AN: 10566

Middle Eastern (MID) AF: 0.446 AC: 131 AN: 294

European-Non Finnish (NFE) AF: 0.347 AC: 23553 AN: 67944

Other (OTH) AF: 0.346 AC: 731 AN: 2112

Alfa AF: 0.321 Hom.: 3422

Bravo AF: 0.281

Asia WGS AF: 0.345 AC: 1198 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.2
DANN	Benign	0.68
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs3093216; hg19: chr19-15987737;