rs159291

Variant names:

• chr17-34374108-G-A
• rs159291

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 0.415 in 151,908 control chromosomes in the GnomAD database, including 13,611 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 0.41 (13611 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.266
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.535 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: 0.415 AC: 62960 AN: 151788 Hom.: 13595 Cov.: 32

Gnomad AFR AF: 0.300

Gnomad AMI AF: 0.468

Gnomad AMR AF: 0.544

Gnomad ASJ AF: 0.394

Gnomad EAS AF: 0.523

Gnomad SAS AF: 0.487

Gnomad FIN AF: 0.477

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.433

Gnomad OTH AF: 0.419

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

GnomAD4 genome AF: 0.415 AC: 63017 AN: 151908 Hom.: 13611 Cov.: 32 AF XY: 0.421 AC XY: 31236 AN XY: 74218

African (AFR) AF: 0.300 AC: 12432 AN: 41436

American (AMR) AF: 0.544 AC: 8314 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.394 AC: 1364 AN: 3466

East Asian (EAS) AF: 0.524 AC: 2696 AN: 5144

South Asian (SAS) AF: 0.486 AC: 2339 AN: 4816

European-Finnish (FIN) AF: 0.477 AC: 5013 AN: 10518

Middle Eastern (MID) AF: 0.354 AC: 104 AN: 294

European-Non Finnish (NFE) AF: 0.433 AC: 29444 AN: 67944

Other (OTH) AF: 0.420 AC: 886 AN: 2110

Alfa AF: 0.436 Hom.: 3786

Bravo AF: 0.416

Asia WGS AF: 0.473 AC: 1643 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.2
DANN	Benign	0.72
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs159291; hg19: chr17-32701127;