17-34285425-A-G

Variant names:

• chr17-34285425-A-G
• rs17809012

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 0.402 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
• Publications: 32 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.340 AC: 14026 AN: 41284

American (AMR) AF: 0.337 AC: 5138 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.466 AC: 1614 AN: 3464

East Asian (EAS) AF: 0.360 AC: 1845 AN: 5132

South Asian (SAS) AF: 0.465 AC: 2215 AN: 4762

European-Finnish (FIN) AF: 0.431 AC: 4532 AN: 10520

Middle Eastern (MID) AF: 0.373 AC: 109 AN: 292

European-Non Finnish (NFE) AF: 0.447 AC: 30303 AN: 67866

Other (OTH) AF: 0.401 AC: 844 AN: 2104

Alfa AF: 0.430 Hom.: 56685

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
PhyloP100		-2.2
PromoterAI		-0.00080	Neutral

Splicing

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

Other links and lift over

dbSNP: rs17809012; hg19: chr17-32612444;