17-34285425-A-G

Variant names:

• chr17-34285425-A-G
• rs17809012

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 0.402 in 151,578 control chromosomes in the GnomAD database, including 12,477 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 0.40 (12477 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.20

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.449 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: 0.402 AC: 60835 AN: 151460 Hom.: 12465 Cov.: 30

Gnomad AFR AF: 0.339

Gnomad AMI AF: 0.277

Gnomad AMR AF: 0.338

Gnomad ASJ AF: 0.466

Gnomad EAS AF: 0.360

Gnomad SAS AF: 0.467

Gnomad FIN AF: 0.431

Gnomad MID AF: 0.357

Gnomad NFE AF: 0.446

Gnomad OTH AF: 0.398

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

GnomAD4 genome AF: 0.402 AC: 60878 AN: 151578 Hom.: 12477 Cov.: 30 AF XY: 0.401 AC XY: 29698 AN XY: 74028

Gnomad4 AFR AF: 0.340

Gnomad4 AMR AF: 0.337

Gnomad4 ASJ AF: 0.466

Gnomad4 EAS AF: 0.360

Gnomad4 SAS AF: 0.465

Gnomad4 FIN AF: 0.431

Gnomad4 NFE AF: 0.447

Gnomad4 OTH AF: 0.401

Alfa AF: 0.433 Hom.: 24300

Bravo AF: 0.388

Asia WGS AF: 0.421 AC: 1464 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	0.15
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17809012; hg19: chr17-32612444;