rs17084228

Positions:

• chr13-26503403-G-A

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;