rs11022713

Variant names:

• chr11-13217783-A-G
• rs11022713

Your query was ambiguous. Multiple possible variants found:

• chr11-13217783-A-G
• chr11-13217783-A-T

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 0.235 in 152,098 control chromosomes in the GnomAD database, including 4,505 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 0.23 (4505 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.99
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.446 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: 0.235 AC: 35726 AN: 151980 Hom.: 4505 Cov.: 32

Gnomad AFR AF: 0.183

Gnomad AMI AF: 0.319

Gnomad AMR AF: 0.266

Gnomad ASJ AF: 0.145

Gnomad EAS AF: 0.462

Gnomad SAS AF: 0.261

Gnomad FIN AF: 0.199

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.251

Gnomad OTH AF: 0.200

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

GnomAD4 genome AF: 0.235 AC: 35728 AN: 152098 Hom.: 4505 Cov.: 32 AF XY: 0.234 AC XY: 17365 AN XY: 74358

African (AFR) AF: 0.183 AC: 7598 AN: 41488

American (AMR) AF: 0.266 AC: 4061 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.145 AC: 503 AN: 3468

East Asian (EAS) AF: 0.461 AC: 2387 AN: 5176

South Asian (SAS) AF: 0.259 AC: 1245 AN: 4816

European-Finnish (FIN) AF: 0.199 AC: 2104 AN: 10580

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.251 AC: 17083 AN: 67976

Other (OTH) AF: 0.199 AC: 420 AN: 2110

Alfa AF: 0.244 Hom.: 20221

Bravo AF: 0.235

Asia WGS AF: 0.344 AC: 1198 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.15
DANN	Benign	0.40
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs11022713; hg19: chr11-13239330;