rs17099726

Variant names:

• chr11-102881122-T-G
• rs17099726

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 0.051 in 144,668 control chromosomes in the GnomAD database, including 780 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 0.051 (780 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.38

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0596 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: 0.0510 AC: 7377 AN: 144566 Hom.: 778 Cov.: 29

Gnomad AFR AF: 0.0470

Gnomad AMI AF: 0.0504

Gnomad AMR AF: 0.0334

Gnomad ASJ AF: 0.0608

Gnomad EAS AF: 0.0274

Gnomad SAS AF: 0.0655

Gnomad FIN AF: 0.0535

Gnomad MID AF: 0.105

Gnomad NFE AF: 0.0570

Gnomad OTH AF: 0.0408

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

GnomAD4 genome AF: 0.0510 AC: 7384 AN: 144668 Hom.: 780 Cov.: 29 AF XY: 0.0498 AC XY: 3525 AN XY: 70734

Gnomad4 AFR AF: 0.0471

Gnomad4 AMR AF: 0.0334

Gnomad4 ASJ AF: 0.0608

Gnomad4 EAS AF: 0.0275

Gnomad4 SAS AF: 0.0657

Gnomad4 FIN AF: 0.0535

Gnomad4 NFE AF: 0.0570

Gnomad4 OTH AF: 0.0399

Alfa AF: 0.0619 Hom.: 160

Asia WGS AF: 0.0510 AC: 174 AN: 3384

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.33
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: rs17099726; hg19: chr11-102751852;