11-17717017-C-T

Variant names:

• chr11-17717017-C-T
• rs2249104

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 0.106 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.106 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

Gnomad4 AFR AF: 0.153

Gnomad4 AMR AF: 0.0896

Gnomad4 ASJ AF: 0.0738

Gnomad4 EAS AF: 0.00964

Gnomad4 SAS AF: 0.247

Gnomad4 FIN AF: 0.0653

Gnomad4 NFE AF: 0.0872

Gnomad4 OTH AF: 0.113

Alfa AF: 0.0828 Hom.: 618

Bravo AF: 0.105

Asia WGS AF: 0.134 AC: 469 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2249104; hg19: chr11-17738564;