rs17289394

Variant names:

• chr13-46899085-G-A
• rs17289394

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 0.325 in 152,076 control chromosomes in the GnomAD database, including 9,372 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 0.32 (9372 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.296

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.404 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: 0.325 AC: 49341 AN: 151958 Hom.: 9372 Cov.: 32

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.668

Gnomad AMR AF: 0.377

Gnomad ASJ AF: 0.229

Gnomad EAS AF: 0.104

Gnomad SAS AF: 0.285

Gnomad FIN AF: 0.497

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.408

Gnomad OTH AF: 0.288

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

GnomAD4 genome AF: 0.325 AC: 49362 AN: 152076 Hom.: 9372 Cov.: 32 AF XY: 0.327 AC XY: 24267 AN XY: 74320

Gnomad4 AFR AF: 0.161

Gnomad4 AMR AF: 0.377

Gnomad4 ASJ AF: 0.229

Gnomad4 EAS AF: 0.104

Gnomad4 SAS AF: 0.286

Gnomad4 FIN AF: 0.497

Gnomad4 NFE AF: 0.408

Gnomad4 OTH AF: 0.285

Alfa AF: 0.371 Hom.: 14827

Bravo AF: 0.308

Asia WGS AF: 0.180 AC: 625 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.2
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17289394; hg19: chr13-47473220;