chr11-109114778-T-C

Variant names:

• chr11-109114778-T-C
• rs17633211

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.0374 in 152,336 control chromosomes in the GnomAD database, including 142 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 0.037 (142 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0890
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.28).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.109 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: 0.0375 AC: 5704 AN: 152218 Hom.: 141 Cov.: 32

Gnomad AFR AF: 0.00885

Gnomad AMI AF: 0.0473

Gnomad AMR AF: 0.0527

Gnomad ASJ AF: 0.0625

Gnomad EAS AF: 0.0227

Gnomad SAS AF: 0.117

Gnomad FIN AF: 0.0590

Gnomad MID AF: 0.0350

Gnomad NFE AF: 0.0420

Gnomad OTH AF: 0.0439

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

GnomAD4 genome AF: 0.0374 AC: 5703 AN: 152336 Hom.: 142 Cov.: 32 AF XY: 0.0397 AC XY: 2956 AN XY: 74490

African (AFR) AF: 0.00890 AC: 370 AN: 41586

American (AMR) AF: 0.0526 AC: 805 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0625 AC: 217 AN: 3472

East Asian (EAS) AF: 0.0227 AC: 118 AN: 5190

South Asian (SAS) AF: 0.117 AC: 563 AN: 4826

European-Finnish (FIN) AF: 0.0590 AC: 626 AN: 10614

Middle Eastern (MID) AF: 0.0342 AC: 10 AN: 292

European-Non Finnish (NFE) AF: 0.0420 AC: 2860 AN: 68032

Other (OTH) AF: 0.0430 AC: 91 AN: 2116

Alfa AF: 0.0396 Hom.: 26

Bravo AF: 0.0341

Asia WGS AF: 0.0510 AC: 176 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.28
CADD	Benign	12
DANN	Benign	0.89
PhyloP100		-0.089

Splicing

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

Other links and lift over

dbSNP: rs17633211; hg19: chr11-108985505;