rs11781082

Variant names:

• chr8-142918485-G-A
• rs11781082

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 152,034 control chromosomes in the GnomAD database, including 3,179 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 (3179 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.358

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.25 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: 0.182 AC: 27586 AN: 151916 Hom.: 3177 Cov.: 31

Gnomad AFR AF: 0.0524

Gnomad AMI AF: 0.315

Gnomad AMR AF: 0.228

Gnomad ASJ AF: 0.221

Gnomad EAS AF: 0.0973

Gnomad SAS AF: 0.0880

Gnomad FIN AF: 0.220

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.253

Gnomad OTH AF: 0.192

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

GnomAD4 genome AF: 0.181 AC: 27594 AN: 152034 Hom.: 3179 Cov.: 31 AF XY: 0.177 AC XY: 13122 AN XY: 74318

Gnomad4 AFR AF: 0.0523

Gnomad4 AMR AF: 0.228

Gnomad4 ASJ AF: 0.221

Gnomad4 EAS AF: 0.0978

Gnomad4 SAS AF: 0.0872

Gnomad4 FIN AF: 0.220

Gnomad4 NFE AF: 0.253

Gnomad4 OTH AF: 0.198

Alfa AF: 0.234 Hom.: 4281

Bravo AF: 0.184

Asia WGS AF: 0.132 AC: 458 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.9
DANN	Benign	0.23

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11781082; hg19: chr8-143999901;