11-17717017-C-T

Variant names:

• chr11-17717017-C-T
• rs2249104

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 0.106 in 152,232 control chromosomes in the GnomAD database, including 1,033 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 0.11 (1033 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0120
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.235 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.106 AC: 16143 AN: 152114 Hom.: 1028 Cov.: 33

Gnomad AFR AF: 0.153

Gnomad AMI AF: 0.0614

Gnomad AMR AF: 0.0899

Gnomad ASJ AF: 0.0738

Gnomad EAS AF: 0.00962

Gnomad SAS AF: 0.248

Gnomad FIN AF: 0.0653

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.0871

Gnomad OTH AF: 0.112

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

GnomAD4 genome AF: 0.106 AC: 16178 AN: 152232 Hom.: 1033 Cov.: 33 AF XY: 0.107 AC XY: 7989 AN XY: 74432

African (AFR) AF: 0.153 AC: 6355 AN: 41506

American (AMR) AF: 0.0896 AC: 1370 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0738 AC: 256 AN: 3470

East Asian (EAS) AF: 0.00964 AC: 50 AN: 5186

South Asian (SAS) AF: 0.247 AC: 1190 AN: 4822

European-Finnish (FIN) AF: 0.0653 AC: 693 AN: 10616

Middle Eastern (MID) AF: 0.137 AC: 40 AN: 292

European-Non Finnish (NFE) AF: 0.0872 AC: 5929 AN: 68018

Other (OTH) AF: 0.113 AC: 239 AN: 2112

Alfa AF: 0.0868 Hom.: 885

Bravo AF: 0.105

Asia WGS AF: 0.134 AC: 469 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.4
DANN	Benign	0.53
PhyloP100		0.012

Splicing

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

Other links and lift over

dbSNP: rs2249104; hg19: chr11-17738564;