chr11-94538497-C-A

Variant names:

• chr11-94538497-C-A
• rs11020821

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 0.271 in 150,982 control chromosomes in the GnomAD database, including 6,086 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 0.27 (6086 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.617
• Publications: 12 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.387 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: 0.271 AC: 40910 AN: 150904 Hom.: 6067 Cov.: 31

Gnomad AFR AF: 0.392

Gnomad AMI AF: 0.109

Gnomad AMR AF: 0.178

Gnomad ASJ AF: 0.184

Gnomad EAS AF: 0.278

Gnomad SAS AF: 0.147

Gnomad FIN AF: 0.297

Gnomad MID AF: 0.198

Gnomad NFE AF: 0.232

Gnomad OTH AF: 0.232

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

GnomAD4 genome AF: 0.271 AC: 40963 AN: 150982 Hom.: 6086 Cov.: 31 AF XY: 0.272 AC XY: 19996 AN XY: 73614

African (AFR) AF: 0.392 AC: 16097 AN: 41032

American (AMR) AF: 0.178 AC: 2697 AN: 15168

Ashkenazi Jewish (ASJ) AF: 0.184 AC: 637 AN: 3470

East Asian (EAS) AF: 0.279 AC: 1434 AN: 5144

South Asian (SAS) AF: 0.147 AC: 701 AN: 4772

European-Finnish (FIN) AF: 0.297 AC: 3039 AN: 10226

Middle Eastern (MID) AF: 0.194 AC: 55 AN: 284

European-Non Finnish (NFE) AF: 0.232 AC: 15723 AN: 67896

Other (OTH) AF: 0.231 AC: 481 AN: 2082

Alfa AF: 0.244 Hom.: 9154

Bravo AF: 0.270

Asia WGS AF: 0.235 AC: 819 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.71
DANN	Benign	0.32
PhyloP100		-0.62

Splicing

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

Other links and lift over

dbSNP: rs11020821; hg19: chr11-94271663;