rs17706334

chr11-109110137-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 0.0384 in 152,302 control chromosomes in the GnomAD database, including 144 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 (144 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.367

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• 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: 5843 AN: 152184 Hom.: 143 Cov.: 31

Gnomad AFR AF: 0.00914

Gnomad AMI AF: 0.0473

Gnomad AMR AF: 0.0536

Gnomad ASJ AF: 0.0678

Gnomad EAS AF: 0.0227

Gnomad SAS AF: 0.114

Gnomad FIN AF: 0.0593

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0437

Gnomad OTH AF: 0.0436

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

GnomAD4 genome AF: 0.0384 AC: 5843 AN: 152302 Hom.: 144 Cov.: 31 AF XY: 0.0404 AC XY: 3006 AN XY: 74474

Gnomad4 AFR AF: 0.00919

Gnomad4 AMR AF: 0.0535

Gnomad4 ASJ AF: 0.0678

Gnomad4 EAS AF: 0.0227

Gnomad4 SAS AF: 0.114

Gnomad4 FIN AF: 0.0593

Gnomad4 NFE AF: 0.0436

Gnomad4 OTH AF: 0.0427

Alfa AF: 0.0393 Hom.: 19

Bravo AF: 0.0351

Asia WGS AF: 0.0530 AC: 184 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	0.41
Dann	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17706334; hg19: chr11-108980864;