rs17084228

Variant names:

• chr13-26503403-G-A
• rs17084228

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 0.21 in 152,116 control chromosomes in the GnomAD database, including 3,701 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 0.21 (3701 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.86

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.285 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: 0.209 AC: 31835 AN: 151998 Hom.: 3696 Cov.: 33

Gnomad AFR AF: 0.286

Gnomad AMI AF: 0.0866

Gnomad AMR AF: 0.292

Gnomad ASJ AF: 0.122

Gnomad EAS AF: 0.159

Gnomad SAS AF: 0.137

Gnomad FIN AF: 0.139

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.171

Gnomad OTH AF: 0.202

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

GnomAD4 genome AF: 0.210 AC: 31870 AN: 152116 Hom.: 3701 Cov.: 33 AF XY: 0.207 AC XY: 15424 AN XY: 74376

Gnomad4 AFR AF: 0.286

Gnomad4 AMR AF: 0.292

Gnomad4 ASJ AF: 0.122

Gnomad4 EAS AF: 0.158

Gnomad4 SAS AF: 0.138

Gnomad4 FIN AF: 0.139

Gnomad4 NFE AF: 0.171

Gnomad4 OTH AF: 0.205

Alfa AF: 0.189 Hom.: 1110

Bravo AF: 0.228

Asia WGS AF: 0.190 AC: 659 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.2
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17084228; hg19: chr13-27077540;