rs11225400

chr11-102731991-C-A

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.0476

Gnomad4 AMR AF: 0.195

Gnomad4 ASJ AF: 0.183

Gnomad4 EAS AF: 0.0935

Gnomad4 SAS AF: 0.150

Gnomad4 FIN AF: 0.238

Gnomad4 NFE AF: 0.254

Gnomad4 OTH AF: 0.173

Alfa AF: 0.218 Hom.: 526

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11225400; hg19: chr11-102602722;