17-34266646-A-G

Variant names:

• chr17-34266646-A-G
• rs3091315

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 0.335 in 152,020 control chromosomes in the GnomAD database, including 9,074 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 0.34 (9074 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.26
• Publications: 56 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.538 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: 0.335 AC: 50923 AN: 151902 Hom.: 9052 Cov.: 32

Gnomad AFR AF: 0.369

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.450

Gnomad ASJ AF: 0.284

Gnomad EAS AF: 0.554

Gnomad SAS AF: 0.344

Gnomad FIN AF: 0.344

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.276

Gnomad OTH AF: 0.321

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

GnomAD4 genome AF: 0.335 AC: 50989 AN: 152020 Hom.: 9074 Cov.: 32 AF XY: 0.342 AC XY: 25394 AN XY: 74302

African (AFR) AF: 0.370 AC: 15320 AN: 41458

American (AMR) AF: 0.451 AC: 6898 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.284 AC: 985 AN: 3470

East Asian (EAS) AF: 0.555 AC: 2859 AN: 5154

South Asian (SAS) AF: 0.345 AC: 1658 AN: 4812

European-Finnish (FIN) AF: 0.344 AC: 3631 AN: 10564

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.276 AC: 18748 AN: 67958

Other (OTH) AF: 0.319 AC: 674 AN: 2112

Alfa AF: 0.298 Hom.: 21691

Bravo AF: 0.346

Asia WGS AF: 0.454 AC: 1576 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	5.4
DANN	Benign	0.87
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs3091315; hg19: chr17-32593665;