rs3091315

Variant names:

• chr17-34266646-A-G
• rs3091315

Your query was ambiguous. Multiple possible variants found:

• chr17-34266646-A-G
• chr17-34266646-A-T

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 0.335 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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.370

Gnomad4 AMR AF: 0.451

Gnomad4 ASJ AF: 0.284

Gnomad4 EAS AF: 0.555

Gnomad4 SAS AF: 0.345

Gnomad4 FIN AF: 0.344

Gnomad4 NFE AF: 0.276

Gnomad4 OTH AF: 0.319

Alfa AF: 0.294 Hom.: 8433

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3091315; hg19: chr17-32593665;