rs8106239

Variant names:

• chr19-35594456-A-C
• rs8106239

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 0.23 in 152,034 control chromosomes in the GnomAD database, including 4,245 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 0.23 (4245 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.181

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.323 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: 0.230 AC: 34925 AN: 151916 Hom.: 4245 Cov.: 31

Gnomad AFR AF: 0.236

Gnomad AMI AF: 0.101

Gnomad AMR AF: 0.323

Gnomad ASJ AF: 0.160

Gnomad EAS AF: 0.336

Gnomad SAS AF: 0.0766

Gnomad FIN AF: 0.142

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.227

Gnomad OTH AF: 0.240

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

GnomAD4 genome AF: 0.230 AC: 34930 AN: 152034 Hom.: 4245 Cov.: 31 AF XY: 0.226 AC XY: 16773 AN XY: 74318

Gnomad4 AFR AF: 0.236

Gnomad4 AMR AF: 0.323

Gnomad4 ASJ AF: 0.160

Gnomad4 EAS AF: 0.336

Gnomad4 SAS AF: 0.0757

Gnomad4 FIN AF: 0.142

Gnomad4 NFE AF: 0.227

Gnomad4 OTH AF: 0.238

Alfa AF: 0.214 Hom.: 1601

Bravo AF: 0.249

Asia WGS AF: 0.179 AC: 623 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.1
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8106239; hg19: chr19-36085358;