rs9580272

Variant names:

• chr13-22002313-A-G
• rs9580272

Your query was ambiguous. Multiple possible variants found:

• chr13-22002313-A-G
• chr13-22002313-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 0.099 in 152,176 control chromosomes in the GnomAD database, including 1,049 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 0.099 (1049 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0950

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.208 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: 0.0989 AC: 15034 AN: 152058 Hom.: 1049 Cov.: 32

Gnomad AFR AF: 0.187

Gnomad AMI AF: 0.0231

Gnomad AMR AF: 0.0566

Gnomad ASJ AF: 0.0795

Gnomad EAS AF: 0.0508

Gnomad SAS AF: 0.219

Gnomad FIN AF: 0.0426

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0618

Gnomad OTH AF: 0.0807

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

GnomAD4 genome AF: 0.0990 AC: 15060 AN: 152176 Hom.: 1049 Cov.: 32 AF XY: 0.0997 AC XY: 7417 AN XY: 74406

Gnomad4 AFR AF: 0.186

Gnomad4 AMR AF: 0.0565

Gnomad4 ASJ AF: 0.0795

Gnomad4 EAS AF: 0.0512

Gnomad4 SAS AF: 0.219

Gnomad4 FIN AF: 0.0426

Gnomad4 NFE AF: 0.0618

Gnomad4 OTH AF: 0.0836

Alfa AF: 0.0675 Hom.: 530

Bravo AF: 0.101

Asia WGS AF: 0.160 AC: 556 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.75
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9580272; hg19: chr13-22576452;