rs9564966

Variant names:

• chr13-73322084-A-G
• rs9564966

Your query was ambiguous. Multiple possible variants found:

• chr13-73322084-A-G
• chr13-73322084-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 0.525 in 151,794 control chromosomes in the GnomAD database, including 24,477 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 0.53 (24477 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0590

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.674 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: 0.526 AC: 79727 AN: 151678 Hom.: 24487 Cov.: 31

Gnomad AFR AF: 0.180

Gnomad AMI AF: 0.513

Gnomad AMR AF: 0.610

Gnomad ASJ AF: 0.571

Gnomad EAS AF: 0.568

Gnomad SAS AF: 0.660

Gnomad FIN AF: 0.665

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.680

Gnomad OTH AF: 0.530

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

GnomAD4 genome AF: 0.525 AC: 79714 AN: 151794 Hom.: 24477 Cov.: 31 AF XY: 0.527 AC XY: 39119 AN XY: 74186

Gnomad4 AFR AF: 0.180

Gnomad4 AMR AF: 0.610

Gnomad4 ASJ AF: 0.571

Gnomad4 EAS AF: 0.568

Gnomad4 SAS AF: 0.659

Gnomad4 FIN AF: 0.665

Gnomad4 NFE AF: 0.680

Gnomad4 OTH AF: 0.529

Alfa AF: 0.652 Hom.: 65511

Bravo AF: 0.505

Asia WGS AF: 0.585 AC: 2034 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.9
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9564966; hg19: chr13-73896221;