rs11603469

Variant names:

• chr11-13658829-G-A
• rs11603469

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 0.178 in 152,124 control chromosomes in the GnomAD database, including 2,605 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 (2605 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.252

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.201 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: 0.178 AC: 27015 AN: 152006 Hom.: 2600 Cov.: 32

Gnomad AFR AF: 0.125

Gnomad AMI AF: 0.193

Gnomad AMR AF: 0.194

Gnomad ASJ AF: 0.119

Gnomad EAS AF: 0.170

Gnomad SAS AF: 0.130

Gnomad FIN AF: 0.245

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.204

Gnomad OTH AF: 0.151

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

GnomAD4 genome AF: 0.178 AC: 27048 AN: 152124 Hom.: 2605 Cov.: 32 AF XY: 0.178 AC XY: 13257 AN XY: 74366

Gnomad4 AFR AF: 0.125

Gnomad4 AMR AF: 0.194

Gnomad4 ASJ AF: 0.119

Gnomad4 EAS AF: 0.170

Gnomad4 SAS AF: 0.130

Gnomad4 FIN AF: 0.245

Gnomad4 NFE AF: 0.204

Gnomad4 OTH AF: 0.151

Alfa AF: 0.196 Hom.: 492

Bravo AF: 0.172

Asia WGS AF: 0.146 AC: 508 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.6
DANN	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11603469; hg19: chr11-13680376;