rs11225400

Variant names:

• chr11-102731991-C-A
• rs11225400

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 152,176 control chromosomes in the GnomAD database, including 3,083 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 (3083 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.854
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.251 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: 27172 AN: 152058 Hom.: 3080 Cov.: 32

Gnomad AFR AF: 0.0477

Gnomad AMI AF: 0.222

Gnomad AMR AF: 0.195

Gnomad ASJ AF: 0.183

Gnomad EAS AF: 0.0933

Gnomad SAS AF: 0.150

Gnomad FIN AF: 0.238

Gnomad MID AF: 0.140

Gnomad NFE AF: 0.254

Gnomad OTH AF: 0.176

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

GnomAD4 genome AF: 0.179 AC: 27174 AN: 152176 Hom.: 3083 Cov.: 32 AF XY: 0.177 AC XY: 13180 AN XY: 74376

African (AFR) AF: 0.0476 AC: 1976 AN: 41544

American (AMR) AF: 0.195 AC: 2978 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.183 AC: 636 AN: 3468

East Asian (EAS) AF: 0.0935 AC: 485 AN: 5186

South Asian (SAS) AF: 0.150 AC: 725 AN: 4824

European-Finnish (FIN) AF: 0.238 AC: 2509 AN: 10564

Middle Eastern (MID) AF: 0.140 AC: 41 AN: 292

European-Non Finnish (NFE) AF: 0.254 AC: 17256 AN: 68006

Other (OTH) AF: 0.173 AC: 366 AN: 2110

Alfa AF: 0.211 Hom.: 527

Bravo AF: 0.173

Asia WGS AF: 0.104 AC: 360 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.44
DANN	Benign	0.56
PhyloP100		-0.85

Splicing

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

Other links and lift over

dbSNP: rs11225400; hg19: chr11-102602722;