rs159319

Variant names:

• chr17-34359668-A-G
• rs159319

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 0.39 in 152,090 control chromosomes in the GnomAD database, including 12,302 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 0.39 (12302 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.98
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.515 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: 0.390 AC: 59218 AN: 151972 Hom.: 12291 Cov.: 33

Gnomad AFR AF: 0.244

Gnomad AMI AF: 0.458

Gnomad AMR AF: 0.524

Gnomad ASJ AF: 0.369

Gnomad EAS AF: 0.528

Gnomad SAS AF: 0.449

Gnomad FIN AF: 0.482

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.419

Gnomad OTH AF: 0.399

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

GnomAD4 genome AF: 0.390 AC: 59251 AN: 152090 Hom.: 12302 Cov.: 33 AF XY: 0.396 AC XY: 29447 AN XY: 74356

African (AFR) AF: 0.244 AC: 10104 AN: 41494

American (AMR) AF: 0.525 AC: 8018 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.369 AC: 1280 AN: 3470

East Asian (EAS) AF: 0.529 AC: 2732 AN: 5164

South Asian (SAS) AF: 0.449 AC: 2165 AN: 4822

European-Finnish (FIN) AF: 0.482 AC: 5104 AN: 10582

Middle Eastern (MID) AF: 0.350 AC: 103 AN: 294

European-Non Finnish (NFE) AF: 0.419 AC: 28485 AN: 67964

Other (OTH) AF: 0.399 AC: 842 AN: 2112

Alfa AF: 0.403 Hom.: 2505

Bravo AF: 0.386

Asia WGS AF: 0.461 AC: 1604 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.0050
DANN	Benign	0.36
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs159319; hg19: chr17-32686687;