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. The variant received -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
• Publications: 19 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.180 AC: 7424 AN: 41290

American (AMR) AF: 0.610 AC: 9309 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.571 AC: 1977 AN: 3462

East Asian (EAS) AF: 0.568 AC: 2938 AN: 5172

South Asian (SAS) AF: 0.659 AC: 3160 AN: 4798

European-Finnish (FIN) AF: 0.665 AC: 7021 AN: 10562

Middle Eastern (MID) AF: 0.459 AC: 135 AN: 294

European-Non Finnish (NFE) AF: 0.680 AC: 46164 AN: 67928

Other (OTH) AF: 0.529 AC: 1118 AN: 2112

Alfa AF: 0.631 Hom.: 134398

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
PhyloP100		-0.059

Splicing

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

Other links and lift over

dbSNP: rs9564966; hg19: chr13-73896221;