rs9573163

Variant names:

• chr13-73334709-C-G
• rs9573163

Your query was ambiguous. Multiple possible variants found:

• chr13-73334709-C-G
• chr13-73334709-C-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 0.523 in 152,082 control chromosomes in the GnomAD database, including 24,413 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 0.52 (24413 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.230
• Publications: 24 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• 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: 0.524 AC: 79591 AN: 151964 Hom.: 24422 Cov.: 32

Gnomad AFR AF: 0.178

Gnomad AMI AF: 0.512

Gnomad AMR AF: 0.609

Gnomad ASJ AF: 0.571

Gnomad EAS AF: 0.568

Gnomad SAS AF: 0.655

Gnomad FIN AF: 0.661

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.679

Gnomad OTH AF: 0.528

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

GnomAD4 genome AF: 0.523 AC: 79580 AN: 152082 Hom.: 24413 Cov.: 32 AF XY: 0.525 AC XY: 39042 AN XY: 74354

African (AFR) AF: 0.177 AC: 7358 AN: 41490

American (AMR) AF: 0.609 AC: 9292 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.571 AC: 1981 AN: 3470

East Asian (EAS) AF: 0.568 AC: 2923 AN: 5148

South Asian (SAS) AF: 0.654 AC: 3155 AN: 4822

European-Finnish (FIN) AF: 0.661 AC: 6990 AN: 10578

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

European-Non Finnish (NFE) AF: 0.679 AC: 46167 AN: 67994

Other (OTH) AF: 0.527 AC: 1113 AN: 2112

Alfa AF: 0.645 Hom.: 17850

Bravo AF: 0.504

Asia WGS AF: 0.584 AC: 2033 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	0.21
DANN	Benign	0.58
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs9573163; hg19: chr13-73908846;