rs11603089

Variant names:

• chr11-18260504-A-G
• rs11603089

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 0.159 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
• Publications: 19 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.0637 AC: 2644 AN: 41488

American (AMR) AF: 0.210 AC: 3214 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.187 AC: 649 AN: 3470

East Asian (EAS) AF: 0.220 AC: 1137 AN: 5176

South Asian (SAS) AF: 0.135 AC: 648 AN: 4806

European-Finnish (FIN) AF: 0.131 AC: 1383 AN: 10574

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.204 AC: 13894 AN: 67984

Other (OTH) AF: 0.163 AC: 345 AN: 2112

Alfa AF: 0.190 Hom.: 5317

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
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs11603089; hg19: chr11-18282051;