rs9579199

Variant names:

• chr13-28590646-G-A
• rs9579199

Your query was ambiguous. Multiple possible variants found:

• chr13-28590646-G-A
• chr13-28590646-G-C

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 0.738 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.738 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

Gnomad4 AFR AF: 0.836

Gnomad4 AMR AF: 0.708

Gnomad4 ASJ AF: 0.773

Gnomad4 EAS AF: 0.490

Gnomad4 SAS AF: 0.706

Gnomad4 FIN AF: 0.603

Gnomad4 NFE AF: 0.724

Gnomad4 OTH AF: 0.746

Alfa AF: 0.726 Hom.: 56763

Bravo AF: 0.747

Asia WGS AF: 0.571 AC: 1990 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9579199; hg19: chr13-29164783;