rs1517057

Variant names:

• chr3-166726225-C-T
• rs1517057

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.691 AC: 28645 AN: 41432

American (AMR) AF: 0.349 AC: 5333 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.310 AC: 1074 AN: 3468

East Asian (EAS) AF: 0.259 AC: 1332 AN: 5148

South Asian (SAS) AF: 0.375 AC: 1804 AN: 4814

European-Finnish (FIN) AF: 0.355 AC: 3735 AN: 10524

Middle Eastern (MID) AF: 0.384 AC: 113 AN: 294

European-Non Finnish (NFE) AF: 0.395 AC: 26857 AN: 67944

Other (OTH) AF: 0.423 AC: 894 AN: 2112

Alfa AF: 0.412 Hom.: 49200

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
PhyloP100		-2.6

Splicing

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

Other links and lift over

dbSNP: rs1517057; hg19: chr3-166444013;