rs17117113

Variant names:

• chr5-155215926-T-C
• rs17117113

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 0.123 in 152,188 control chromosomes in the GnomAD database, including 1,350 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 0.12 (1350 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.687

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.163 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: 0.123 AC: 18704 AN: 152070 Hom.: 1349 Cov.: 32

Gnomad AFR AF: 0.0327

Gnomad AMI AF: 0.186

Gnomad AMR AF: 0.141

Gnomad ASJ AF: 0.163

Gnomad EAS AF: 0.139

Gnomad SAS AF: 0.157

Gnomad FIN AF: 0.132

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.166

Gnomad OTH AF: 0.131

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

GnomAD4 genome AF: 0.123 AC: 18711 AN: 152188 Hom.: 1350 Cov.: 32 AF XY: 0.123 AC XY: 9177 AN XY: 74398

Gnomad4 AFR AF: 0.0326

Gnomad4 AMR AF: 0.141

Gnomad4 ASJ AF: 0.163

Gnomad4 EAS AF: 0.139

Gnomad4 SAS AF: 0.157

Gnomad4 FIN AF: 0.132

Gnomad4 NFE AF: 0.166

Gnomad4 OTH AF: 0.132

Alfa AF: 0.136 Hom.: 245

Bravo AF: 0.118

Asia WGS AF: 0.152 AC: 530 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.1
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17117113; hg19: chr5-154595486;