11-86076782-C-T

Position:

• chr11-86076782-C-T

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 0.723 in 152,076 control chromosomes in the GnomAD database, including 40,457 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 0.72 (40457 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.742

Genes affected

(HGNC:):

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 (AFR) allele frequency at 95% confidence interval = 0.861 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.86076782C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.723 AC: 109892 AN: 151958 Hom.: 40417 Cov.: 32

Gnomad AFR AF: 0.869

Gnomad AMI AF: 0.595

Gnomad AMR AF: 0.667

Gnomad ASJ AF: 0.652

Gnomad EAS AF: 0.493

Gnomad SAS AF: 0.596

Gnomad FIN AF: 0.661

Gnomad MID AF: 0.623

Gnomad NFE AF: 0.690

Gnomad OTH AF: 0.707

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

GnomAD4 genome AF: 0.723 AC: 109991 AN: 152076 Hom.: 40457 Cov.: 32 AF XY: 0.717 AC XY: 53265 AN XY: 74330

Gnomad4 AFR AF: 0.869

Gnomad4 AMR AF: 0.666

Gnomad4 ASJ AF: 0.652

Gnomad4 EAS AF: 0.493

Gnomad4 SAS AF: 0.597

Gnomad4 FIN AF: 0.661

Gnomad4 NFE AF: 0.690

Gnomad4 OTH AF: 0.707

Alfa AF: 0.683 Hom.: 54572

Bravo AF: 0.728

Asia WGS AF: 0.561 AC: 1954 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	8.4
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs536841; hg19: chr11-85787824;