11-72212498-T-G

Variant names:

• chr11-72212498-T-G
• rs11235468

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 0.18 in 152,020 control chromosomes in the GnomAD database, including 2,957 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 (2957 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.953
• Publications: 13 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.313 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: 0.180 AC: 27282 AN: 151902 Hom.: 2938 Cov.: 32

Gnomad AFR AF: 0.284

Gnomad AMI AF: 0.0121

Gnomad AMR AF: 0.152

Gnomad ASJ AF: 0.129

Gnomad EAS AF: 0.325

Gnomad SAS AF: 0.216

Gnomad FIN AF: 0.163

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.117

Gnomad OTH AF: 0.158

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

GnomAD4 genome AF: 0.180 AC: 27338 AN: 152020 Hom.: 2957 Cov.: 32 AF XY: 0.184 AC XY: 13697 AN XY: 74314

African (AFR) AF: 0.285 AC: 11798 AN: 41402

American (AMR) AF: 0.151 AC: 2310 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.129 AC: 449 AN: 3468

East Asian (EAS) AF: 0.326 AC: 1685 AN: 5174

South Asian (SAS) AF: 0.215 AC: 1035 AN: 4812

European-Finnish (FIN) AF: 0.163 AC: 1728 AN: 10582

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.117 AC: 7937 AN: 67976

Other (OTH) AF: 0.166 AC: 351 AN: 2112

Alfa AF: 0.138 Hom.: 6927

Bravo AF: 0.182

Asia WGS AF: 0.312 AC: 1085 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	0.47
DANN	Benign	0.41
PhyloP100		-0.95

Splicing

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

Other links and lift over

dbSNP: rs11235468; hg19: chr11-71923542;