rs17108927

Variant names:

• chr5-148906754-T-C
• rs17108927

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 0.0542 in 152,234 control chromosomes in the GnomAD database, including 269 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 0.054 (269 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.497

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0951 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: 0.0542 AC: 8248 AN: 152116 Hom.: 266 Cov.: 32

Gnomad AFR AF: 0.0977

Gnomad AMI AF: 0.0604

Gnomad AMR AF: 0.0325

Gnomad ASJ AF: 0.0253

Gnomad EAS AF: 0.0553

Gnomad SAS AF: 0.0436

Gnomad FIN AF: 0.0135

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0409

Gnomad OTH AF: 0.0559

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

GnomAD4 genome AF: 0.0542 AC: 8253 AN: 152234 Hom.: 269 Cov.: 32 AF XY: 0.0530 AC XY: 3945 AN XY: 74436

Gnomad4 AFR AF: 0.0976

Gnomad4 AMR AF: 0.0324

Gnomad4 ASJ AF: 0.0253

Gnomad4 EAS AF: 0.0551

Gnomad4 SAS AF: 0.0438

Gnomad4 FIN AF: 0.0135

Gnomad4 NFE AF: 0.0409

Gnomad4 OTH AF: 0.0548

Alfa AF: 0.0478 Hom.: 32

Bravo AF: 0.0596

Asia WGS AF: 0.0510 AC: 177 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.61
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17108927; hg19: chr5-148286317;