11-86156833-A-G

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 0.695 in 152,112 control chromosomes in the GnomAD database, including 37,559 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 0.70 (37559 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.467

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.852 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: 0.695 AC: 105649 AN: 151994 Hom.: 37516 Cov.: 32

Gnomad AFR AF: 0.860

Gnomad AMI AF: 0.521

Gnomad AMR AF: 0.637

Gnomad ASJ AF: 0.610

Gnomad EAS AF: 0.603

Gnomad SAS AF: 0.610

Gnomad FIN AF: 0.647

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.636

Gnomad OTH AF: 0.685

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

GnomAD4 genome AF: 0.695 AC: 105752 AN: 152112 Hom.: 37559 Cov.: 32 AF XY: 0.692 AC XY: 51483 AN XY: 74350

Gnomad4 AFR AF: 0.860

Gnomad4 AMR AF: 0.637

Gnomad4 ASJ AF: 0.610

Gnomad4 EAS AF: 0.602

Gnomad4 SAS AF: 0.612

Gnomad4 FIN AF: 0.647

Gnomad4 NFE AF: 0.636

Gnomad4 OTH AF: 0.684

Alfa AF: 0.701 Hom.: 5438

Bravo AF: 0.700

Asia WGS AF: 0.602 AC: 2095 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	5.2
Dann	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10792832; hg19: chr11-85867875;