rs9564266

Variant names:

• chr13-65584924-A-G
• rs9564266

Your query was ambiguous. Multiple possible variants found:

• chr13-65584924-A-G
• chr13-65584924-A-T

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 0.453 in 151,868 control chromosomes in the GnomAD database, including 16,130 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 0.45 (16130 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.272

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.747 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: 0.453 AC: 68726 AN: 151750 Hom.: 16114 Cov.: 31

Gnomad AFR AF: 0.533

Gnomad AMI AF: 0.309

Gnomad AMR AF: 0.414

Gnomad ASJ AF: 0.433

Gnomad EAS AF: 0.767

Gnomad SAS AF: 0.524

Gnomad FIN AF: 0.454

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.387

Gnomad OTH AF: 0.447

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

GnomAD4 genome AF: 0.453 AC: 68790 AN: 151868 Hom.: 16130 Cov.: 31 AF XY: 0.459 AC XY: 34049 AN XY: 74238

Gnomad4 AFR AF: 0.533

Gnomad4 AMR AF: 0.414

Gnomad4 ASJ AF: 0.433

Gnomad4 EAS AF: 0.767

Gnomad4 SAS AF: 0.523

Gnomad4 FIN AF: 0.454

Gnomad4 NFE AF: 0.387

Gnomad4 OTH AF: 0.451

Alfa AF: 0.398 Hom.: 12114

Bravo AF: 0.455

Asia WGS AF: 0.629 AC: 2183 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.6
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9564266; hg19: chr13-66159056;