rs17099726

Variant names:

• chr11-102881122-T-G
• rs17099726

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 0.051 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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.0471 AC: 1681 AN: 35696

American (AMR) AF: 0.0334 AC: 497 AN: 14886

Ashkenazi Jewish (ASJ) AF: 0.0608 AC: 205 AN: 3372

East Asian (EAS) AF: 0.0275 AC: 138 AN: 5026

South Asian (SAS) AF: 0.0657 AC: 302 AN: 4596

European-Finnish (FIN) AF: 0.0535 AC: 560 AN: 10466

Middle Eastern (MID) AF: 0.105 AC: 29 AN: 276

European-Non Finnish (NFE) AF: 0.0570 AC: 3846 AN: 67430

Other (OTH) AF: 0.0399 AC: 81 AN: 2028

Alfa AF: 0.0608 Hom.: 160

Asia WGS AF: 0.0510 AC: 174 AN: 3384

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.33
DANN	Benign	0.48
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs17099726; hg19: chr11-102751852;