rs11603089

Positions:

• chr11-18260504-A-G

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 0.159 in 152,092 control chromosomes in the GnomAD database, including 2,189 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 0.16 (2189 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.106

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.209 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.159 AC: 24156 AN: 151974 Hom.: 2191 Cov.: 32

Gnomad AFR AF: 0.0638

Gnomad AMI AF: 0.223

Gnomad AMR AF: 0.210

Gnomad ASJ AF: 0.187

Gnomad EAS AF: 0.220

Gnomad SAS AF: 0.134

Gnomad FIN AF: 0.131

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.204

Gnomad OTH AF: 0.167

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

GnomAD4 genome AF: 0.159 AC: 24162 AN: 152092 Hom.: 2189 Cov.: 32 AF XY: 0.155 AC XY: 11535 AN XY: 74334

Gnomad4 AFR AF: 0.0637

Gnomad4 AMR AF: 0.210

Gnomad4 ASJ AF: 0.187

Gnomad4 EAS AF: 0.220

Gnomad4 SAS AF: 0.135

Gnomad4 FIN AF: 0.131

Gnomad4 NFE AF: 0.204

Gnomad4 OTH AF: 0.163

Alfa AF: 0.194 Hom.: 3925

Bravo AF: 0.163

Asia WGS AF: 0.167 AC: 584 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.5
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11603089; hg19: chr11-18282051;