rs17523405

Variant names:

• chr13-27305470-T-C
• rs17523405

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 0.087 in 150,096 control chromosomes in the GnomAD database, including 841 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 0.087 (841 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.342

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 (NFE) allele frequency at 95% confidence interval = 0.121 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: 0.0871 AC: 13058 AN: 149980 Hom.: 841 Cov.: 29

Gnomad AFR AF: 0.0177

Gnomad AMI AF: 0.0872

Gnomad AMR AF: 0.0727

Gnomad ASJ AF: 0.0855

Gnomad EAS AF: 0.00117

Gnomad SAS AF: 0.0305

Gnomad FIN AF: 0.220

Gnomad MID AF: 0.125

Gnomad NFE AF: 0.124

Gnomad OTH AF: 0.0810

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

GnomAD4 genome AF: 0.0870 AC: 13055 AN: 150096 Hom.: 841 Cov.: 29 AF XY: 0.0891 AC XY: 6518 AN XY: 73124

Gnomad4 AFR AF: 0.0176

Gnomad4 AMR AF: 0.0726

Gnomad4 ASJ AF: 0.0855

Gnomad4 EAS AF: 0.00118

Gnomad4 SAS AF: 0.0309

Gnomad4 FIN AF: 0.220

Gnomad4 NFE AF: 0.124

Gnomad4 OTH AF: 0.0797

Alfa AF: 0.116 Hom.: 775

Bravo AF: 0.0733

Asia WGS AF: 0.0180 AC: 64 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	4.0
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17523405; hg19: chr13-27879607;