rs17706334

Variant names:

• chr11-109110137-A-G
• rs17706334

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 0.0384 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
• Publications: 0 publications found

ACMG classification

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.00919 AC: 382 AN: 41580

American (AMR) AF: 0.0535 AC: 818 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0678 AC: 235 AN: 3468

East Asian (EAS) AF: 0.0227 AC: 118 AN: 5188

South Asian (SAS) AF: 0.114 AC: 548 AN: 4818

European-Finnish (FIN) AF: 0.0593 AC: 630 AN: 10616

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0436 AC: 2969 AN: 68024

Other (OTH) AF: 0.0427 AC: 90 AN: 2110

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
PhyloP100		-0.37

Splicing

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

Other links and lift over

dbSNP: rs17706334; hg19: chr11-108980864;