rs1517057

chr3-166726225-C-T

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 0.461 in 151,930 control chromosomes in the GnomAD database, including 17,780 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 0.46 (17780 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.56

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.685 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.461 AC: 70038 AN: 151812 Hom.: 17755 Cov.: 32

Gnomad AFR AF: 0.691

Gnomad AMI AF: 0.358

Gnomad AMR AF: 0.349

Gnomad ASJ AF: 0.310

Gnomad EAS AF: 0.259

Gnomad SAS AF: 0.375

Gnomad FIN AF: 0.355

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.395

Gnomad OTH AF: 0.424

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

GnomAD4 genome AF: 0.461 AC: 70113 AN: 151930 Hom.: 17780 Cov.: 32 AF XY: 0.455 AC XY: 33792 AN XY: 74228

Gnomad4 AFR AF: 0.691

Gnomad4 AMR AF: 0.349

Gnomad4 ASJ AF: 0.310

Gnomad4 EAS AF: 0.259

Gnomad4 SAS AF: 0.375

Gnomad4 FIN AF: 0.355

Gnomad4 NFE AF: 0.395

Gnomad4 OTH AF: 0.423

Alfa AF: 0.397 Hom.: 19160

Bravo AF: 0.471

Asia WGS AF: 0.330 AC: 1150 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	0.37
Dann	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1517057; hg19: chr3-166444013;