rs17523405

chr13-27305470-T-C

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/exons	MANE	UniProt

Ensembl

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