rs11605083

Variant names:

• chr11-15333700-T-C
• rs11605083

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 152,238 control chromosomes in the GnomAD database, including 2,745 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 (2745 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.222 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: 0.180 AC: 27326 AN: 152120 Hom.: 2744 Cov.: 33

Gnomad AFR AF: 0.101

Gnomad AMI AF: 0.116

Gnomad AMR AF: 0.164

Gnomad ASJ AF: 0.211

Gnomad EAS AF: 0.211

Gnomad SAS AF: 0.225

Gnomad FIN AF: 0.171

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.225

Gnomad OTH AF: 0.202

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

GnomAD4 genome AF: 0.179 AC: 27326 AN: 152238 Hom.: 2745 Cov.: 33 AF XY: 0.178 AC XY: 13268 AN XY: 74436

Gnomad4 AFR AF: 0.101

Gnomad4 AMR AF: 0.164

Gnomad4 ASJ AF: 0.211

Gnomad4 EAS AF: 0.211

Gnomad4 SAS AF: 0.225

Gnomad4 FIN AF: 0.171

Gnomad4 NFE AF: 0.225

Gnomad4 OTH AF: 0.198

Alfa AF: 0.216 Hom.: 3754

Bravo AF: 0.176

Asia WGS AF: 0.172 AC: 597 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	3.1
DANN	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11605083; hg19: chr11-15355246;