rs11236682

Variant names:

• chr11-76284088-C-G
• rs11236682

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 0.218 in 152,016 control chromosomes in the GnomAD database, including 3,991 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 0.22 (3991 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.28
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.355 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: 0.218 AC: 33082 AN: 151898 Hom.: 3994 Cov.: 32

Gnomad AFR AF: 0.247

Gnomad AMI AF: 0.320

Gnomad AMR AF: 0.324

Gnomad ASJ AF: 0.152

Gnomad EAS AF: 0.370

Gnomad SAS AF: 0.345

Gnomad FIN AF: 0.222

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.157

Gnomad OTH AF: 0.212

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

GnomAD4 genome AF: 0.218 AC: 33083 AN: 152016 Hom.: 3991 Cov.: 32 AF XY: 0.224 AC XY: 16646 AN XY: 74282

African (AFR) AF: 0.246 AC: 10218 AN: 41456

American (AMR) AF: 0.324 AC: 4957 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.152 AC: 526 AN: 3466

East Asian (EAS) AF: 0.369 AC: 1902 AN: 5152

South Asian (SAS) AF: 0.345 AC: 1665 AN: 4820

European-Finnish (FIN) AF: 0.222 AC: 2342 AN: 10572

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.157 AC: 10692 AN: 67954

Other (OTH) AF: 0.209 AC: 440 AN: 2108

Alfa AF: 0.194 Hom.: 426

Bravo AF: 0.225

Asia WGS AF: 0.305 AC: 1058 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.037
DANN	Benign	0.39
PhyloP100		-3.3

Splicing

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

Other links and lift over

dbSNP: rs11236682; hg19: chr11-75995132;