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. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.186 AC: 7733 AN: 41496

American (AMR) AF: 0.0565 AC: 864 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0795 AC: 276 AN: 3470

East Asian (EAS) AF: 0.0512 AC: 265 AN: 5180

South Asian (SAS) AF: 0.219 AC: 1054 AN: 4802

European-Finnish (FIN) AF: 0.0426 AC: 452 AN: 10604

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0618 AC: 4201 AN: 68016

Other (OTH) AF: 0.0836 AC: 177 AN: 2116

Alfa AF: 0.0736 Hom.: 1504

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
PhyloP100		-0.095

Splicing

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

Other links and lift over

dbSNP: rs9580272; hg19: chr13-22576452;