rs17105869

Variant names:

• chr11-106606364-G-A
• rs17105869

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 0.296 in 151,788 control chromosomes in the GnomAD database, including 8,130 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 0.30 (8130 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.700

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.503 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: 0.296 AC: 44845 AN: 151670 Hom.: 8112 Cov.: 32

Gnomad AFR AF: 0.509

Gnomad AMI AF: 0.0879

Gnomad AMR AF: 0.232

Gnomad ASJ AF: 0.109

Gnomad EAS AF: 0.0375

Gnomad SAS AF: 0.128

Gnomad FIN AF: 0.294

Gnomad MID AF: 0.134

Gnomad NFE AF: 0.226

Gnomad OTH AF: 0.276

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

GnomAD4 genome AF: 0.296 AC: 44914 AN: 151788 Hom.: 8130 Cov.: 32 AF XY: 0.292 AC XY: 21678 AN XY: 74184

Gnomad4 AFR AF: 0.509

Gnomad4 AMR AF: 0.232

Gnomad4 ASJ AF: 0.109

Gnomad4 EAS AF: 0.0374

Gnomad4 SAS AF: 0.128

Gnomad4 FIN AF: 0.294

Gnomad4 NFE AF: 0.226

Gnomad4 OTH AF: 0.274

Alfa AF: 0.223 Hom.: 5638

Bravo AF: 0.303

Asia WGS AF: 0.108 AC: 379 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.39
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17105869; hg19: chr11-106477091;