rs17566649

Variant names:

• chr13-26855065-T-A
• rs17566649

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 0.0494 in 152,312 control chromosomes in the GnomAD database, including 287 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 0.049 (287 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0350

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0727 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: 0.0495 AC: 7532 AN: 152194 Hom.: 286 Cov.: 32

Gnomad AFR AF: 0.0122

Gnomad AMI AF: 0.0263

Gnomad AMR AF: 0.0454

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.000769

Gnomad SAS AF: 0.0319

Gnomad FIN AF: 0.0568

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0744

Gnomad OTH AF: 0.0511

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

GnomAD4 genome AF: 0.0494 AC: 7527 AN: 152312 Hom.: 287 Cov.: 32 AF XY: 0.0483 AC XY: 3598 AN XY: 74482

Gnomad4 AFR AF: 0.0122

Gnomad4 AMR AF: 0.0453

Gnomad4 ASJ AF: 0.103

Gnomad4 EAS AF: 0.000771

Gnomad4 SAS AF: 0.0313

Gnomad4 FIN AF: 0.0568

Gnomad4 NFE AF: 0.0744

Gnomad4 OTH AF: 0.0501

Alfa AF: 0.0611 Hom.: 48

Bravo AF: 0.0462

Asia WGS AF: 0.0220 AC: 75 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.2
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17566649; hg19: chr13-27429202;