rs11217223

Variant names:

• chr11-98852486-A-G
• rs11217223

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 0.0595 in 152,270 control chromosomes in the GnomAD database, including 464 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 0.059 (464 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.164
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.294 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: 0.0594 AC: 9040 AN: 152152 Hom.: 463 Cov.: 32

Gnomad AFR AF: 0.0383

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0859

Gnomad ASJ AF: 0.0507

Gnomad EAS AF: 0.306

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.0768

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0430

Gnomad OTH AF: 0.0665

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

GnomAD4 genome AF: 0.0595 AC: 9059 AN: 152270 Hom.: 464 Cov.: 32 AF XY: 0.0636 AC XY: 4737 AN XY: 74456

African (AFR) AF: 0.0383 AC: 1591 AN: 41570

American (AMR) AF: 0.0861 AC: 1317 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0507 AC: 176 AN: 3468

East Asian (EAS) AF: 0.307 AC: 1584 AN: 5168

South Asian (SAS) AF: 0.101 AC: 489 AN: 4828

European-Finnish (FIN) AF: 0.0768 AC: 814 AN: 10604

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.0430 AC: 2927 AN: 68024

Other (OTH) AF: 0.0687 AC: 145 AN: 2112

Alfa AF: 0.0528 Hom.: 740

Bravo AF: 0.0599

Asia WGS AF: 0.197 AC: 682 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	9.1
DANN	Benign	0.74
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs11217223; hg19: chr11-98723216;