13-28590646-G-A

Variant names:

• chr13-28590646-G-A
• rs9579199

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 0.738 in 152,178 control chromosomes in the GnomAD database, including 41,966 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 0.74 (41966 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.799
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.829 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.738 AC: 112225 AN: 152060 Hom.: 41930 Cov.: 33

Gnomad AFR AF: 0.836

Gnomad AMI AF: 0.765

Gnomad AMR AF: 0.709

Gnomad ASJ AF: 0.773

Gnomad EAS AF: 0.491

Gnomad SAS AF: 0.705

Gnomad FIN AF: 0.603

Gnomad MID AF: 0.755

Gnomad NFE AF: 0.724

Gnomad OTH AF: 0.750

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

GnomAD4 genome AF: 0.738 AC: 112312 AN: 152178 Hom.: 41966 Cov.: 33 AF XY: 0.731 AC XY: 54322 AN XY: 74352

African (AFR) AF: 0.836 AC: 34738 AN: 41542

American (AMR) AF: 0.708 AC: 10836 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.773 AC: 2683 AN: 3472

East Asian (EAS) AF: 0.490 AC: 2533 AN: 5170

South Asian (SAS) AF: 0.706 AC: 3405 AN: 4826

European-Finnish (FIN) AF: 0.603 AC: 6369 AN: 10560

Middle Eastern (MID) AF: 0.750 AC: 219 AN: 292

European-Non Finnish (NFE) AF: 0.724 AC: 49258 AN: 67998

Other (OTH) AF: 0.746 AC: 1575 AN: 2112

Alfa AF: 0.733 Hom.: 102253

Bravo AF: 0.747

Asia WGS AF: 0.571 AC: 1990 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.2
DANN	Benign	0.64
PhyloP100		-0.80

Splicing

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

Other links and lift over

dbSNP: rs9579199; hg19: chr13-29164783;