rs17706299

chr11-109110090-C-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 0.0384 in 152,220 control chromosomes in the GnomAD database, including 145 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 0.038 (145 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.79

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 (SAS) allele frequency at 95% confidence interval = 0.106 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: 0.0384 AC: 5847 AN: 152102 Hom.: 144 Cov.: 32

Gnomad AFR AF: 0.00915

Gnomad AMI AF: 0.0471

Gnomad AMR AF: 0.0537

Gnomad ASJ AF: 0.0680

Gnomad EAS AF: 0.0227

Gnomad SAS AF: 0.114

Gnomad FIN AF: 0.0594

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0437

Gnomad OTH AF: 0.0431

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

GnomAD4 genome AF: 0.0384 AC: 5847 AN: 152220 Hom.: 145 Cov.: 32 AF XY: 0.0405 AC XY: 3012 AN XY: 74446

Gnomad4 AFR AF: 0.00919

Gnomad4 AMR AF: 0.0536

Gnomad4 ASJ AF: 0.0680

Gnomad4 EAS AF: 0.0228

Gnomad4 SAS AF: 0.114

Gnomad4 FIN AF: 0.0594

Gnomad4 NFE AF: 0.0437

Gnomad4 OTH AF: 0.0422

Alfa AF: 0.0394 Hom.: 19

Bravo AF: 0.0351

Asia WGS AF: 0.0530 AC: 183 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	0.030
Dann	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17706299; hg19: chr11-108980817;