rs159291

Positions:

• chr17-34374108-G-A

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 0.415 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.300

Gnomad4 AMR AF: 0.544

Gnomad4 ASJ AF: 0.394

Gnomad4 EAS AF: 0.524

Gnomad4 SAS AF: 0.486

Gnomad4 FIN AF: 0.477

Gnomad4 NFE AF: 0.433

Gnomad4 OTH AF: 0.420

Alfa AF: 0.438 Hom.: 3737

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs159291; hg19: chr17-32701127;