rs159319

Positions:

• chr17-34359668-A-G

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 0.39 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.244

Gnomad4 AMR AF: 0.525

Gnomad4 ASJ AF: 0.369

Gnomad4 EAS AF: 0.529

Gnomad4 SAS AF: 0.449

Gnomad4 FIN AF: 0.482

Gnomad4 NFE AF: 0.419

Gnomad4 OTH AF: 0.399

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs159319; hg19: chr17-32686687;