rs17105932

Variant names:

• chr11-106672739-T-A
• rs17105932

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 0.0723 in 152,230 control chromosomes in the GnomAD database, including 638 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 0.072 (638 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.206

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.136 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: 0.0723 AC: 10995 AN: 152112 Hom.: 635 Cov.: 31

Gnomad AFR AF: 0.135

Gnomad AMI AF: 0.0175

Gnomad AMR AF: 0.142

Gnomad ASJ AF: 0.0294

Gnomad EAS AF: 0.0892

Gnomad SAS AF: 0.0224

Gnomad FIN AF: 0.0446

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0281

Gnomad OTH AF: 0.0789

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

GnomAD4 genome AF: 0.0723 AC: 11007 AN: 152230 Hom.: 638 Cov.: 31 AF XY: 0.0729 AC XY: 5425 AN XY: 74438

Gnomad4 AFR AF: 0.135

Gnomad4 AMR AF: 0.141

Gnomad4 ASJ AF: 0.0294

Gnomad4 EAS AF: 0.0896

Gnomad4 SAS AF: 0.0224

Gnomad4 FIN AF: 0.0446

Gnomad4 NFE AF: 0.0281

Gnomad4 OTH AF: 0.0814

Alfa AF: 0.0509 Hom.: 35

Bravo AF: 0.0846

Asia WGS AF: 0.0680 AC: 234 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.36
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17105932; hg19: chr11-106543465;