rs17797517

Variant names:

• chr3-187747694-T-C
• rs17797517

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 0.233 in 152,148 control chromosomes in the GnomAD database, including 4,865 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 0.23 (4865 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.268

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.53).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.319 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: 0.233 AC: 35388 AN: 152030 Hom.: 4869 Cov.: 33

Gnomad AFR AF: 0.0976

Gnomad AMI AF: 0.315

Gnomad AMR AF: 0.327

Gnomad ASJ AF: 0.185

Gnomad EAS AF: 0.195

Gnomad SAS AF: 0.287

Gnomad FIN AF: 0.335

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.279

Gnomad OTH AF: 0.233

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

GnomAD4 genome AF: 0.233 AC: 35388 AN: 152148 Hom.: 4865 Cov.: 33 AF XY: 0.236 AC XY: 17558 AN XY: 74380

Gnomad4 AFR AF: 0.0974

Gnomad4 AMR AF: 0.326

Gnomad4 ASJ AF: 0.185

Gnomad4 EAS AF: 0.195

Gnomad4 SAS AF: 0.287

Gnomad4 FIN AF: 0.335

Gnomad4 NFE AF: 0.279

Gnomad4 OTH AF: 0.232

Alfa AF: 0.251 Hom.: 1972

Bravo AF: 0.225

Asia WGS AF: 0.263 AC: 913 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.53
CADD	Benign	12
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17797517; hg19: chr3-187465482;