chr11-109110090-C-G

Variant names:

• chr11-109110090-C-G
• rs17706299

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 0.0384 in 152,220 control chromosomes in the GnomAD database, including 145 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 0.038 (145 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.79
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.106 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: 0.0384 AC: 5847 AN: 152102 Hom.: 144 Cov.: 32

Gnomad AFR AF: 0.00915

Gnomad AMI AF: 0.0471

Gnomad AMR AF: 0.0537

Gnomad ASJ AF: 0.0680

Gnomad EAS AF: 0.0227

Gnomad SAS AF: 0.114

Gnomad FIN AF: 0.0594

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0437

Gnomad OTH AF: 0.0431

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

GnomAD4 genome AF: 0.0384 AC: 5847 AN: 152220 Hom.: 145 Cov.: 32 AF XY: 0.0405 AC XY: 3012 AN XY: 74446

African (AFR) AF: 0.00919 AC: 382 AN: 41552

American (AMR) AF: 0.0536 AC: 820 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0680 AC: 236 AN: 3470

East Asian (EAS) AF: 0.0228 AC: 118 AN: 5178

South Asian (SAS) AF: 0.114 AC: 551 AN: 4822

European-Finnish (FIN) AF: 0.0594 AC: 629 AN: 10592

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0437 AC: 2969 AN: 67998

Other (OTH) AF: 0.0422 AC: 89 AN: 2110

Alfa AF: 0.0394 Hom.: 19

Bravo AF: 0.0351

Asia WGS AF: 0.0530 AC: 183 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.030
DANN	Benign	0.34
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs17706299; hg19: chr11-108980817;