11-128946326-G-A

Variant names:

• chr11-128946326-G-A
• rs11221522

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 0.179 in 152,040 control chromosomes in the GnomAD database, including 2,629 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 0.18 (2629 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.07).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.216 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: 0.179 AC: 27242 AN: 151922 Hom.: 2633 Cov.: 33

Gnomad AFR AF: 0.136

Gnomad AMI AF: 0.113

Gnomad AMR AF: 0.115

Gnomad ASJ AF: 0.140

Gnomad EAS AF: 0.118

Gnomad SAS AF: 0.110

Gnomad FIN AF: 0.274

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.219

Gnomad OTH AF: 0.148

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

GnomAD4 genome AF: 0.179 AC: 27244 AN: 152040 Hom.: 2629 Cov.: 33 AF XY: 0.180 AC XY: 13399 AN XY: 74328

African (AFR) AF: 0.136 AC: 5646 AN: 41478

American (AMR) AF: 0.114 AC: 1750 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.140 AC: 486 AN: 3470

East Asian (EAS) AF: 0.118 AC: 610 AN: 5174

South Asian (SAS) AF: 0.110 AC: 528 AN: 4814

European-Finnish (FIN) AF: 0.274 AC: 2888 AN: 10544

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.219 AC: 14889 AN: 67958

Other (OTH) AF: 0.146 AC: 309 AN: 2114

Alfa AF: 0.200 Hom.: 410

Bravo AF: 0.164

Asia WGS AF: 0.106 AC: 372 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.32
DANN	Benign	0.58
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs11221522; hg19: chr11-128816221;