11-86076782-C-T

Variant names:

• chr11-86076782-C-T
• rs536841

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 0.723 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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.742
• Publications: 39 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.869 AC: 36051 AN: 41506

American (AMR) AF: 0.666 AC: 10171 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.652 AC: 2261 AN: 3470

East Asian (EAS) AF: 0.493 AC: 2550 AN: 5170

South Asian (SAS) AF: 0.597 AC: 2878 AN: 4820

European-Finnish (FIN) AF: 0.661 AC: 6976 AN: 10548

Middle Eastern (MID) AF: 0.633 AC: 186 AN: 294

European-Non Finnish (NFE) AF: 0.690 AC: 46884 AN: 67968

Other (OTH) AF: 0.707 AC: 1493 AN: 2112

Alfa AF: 0.692 Hom.: 126081

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
PhyloP100		0.74

Splicing

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

Other links and lift over

dbSNP: rs536841; hg19: chr11-85787824;