rs17105932

chr11-106672739-T-A

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;