rs9578484

Variant names:

• chr13-22648951-A-G
• rs9578484

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 0.209 in 152,142 control chromosomes in the GnomAD database, including 3,663 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 0.21 (3663 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.446

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.303 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: 0.209 AC: 31766 AN: 152024 Hom.: 3660 Cov.: 33

Gnomad AFR AF: 0.308

Gnomad AMI AF: 0.137

Gnomad AMR AF: 0.186

Gnomad ASJ AF: 0.124

Gnomad EAS AF: 0.191

Gnomad SAS AF: 0.121

Gnomad FIN AF: 0.245

Gnomad MID AF: 0.162

Gnomad NFE AF: 0.163

Gnomad OTH AF: 0.174

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

GnomAD4 genome AF: 0.209 AC: 31791 AN: 152142 Hom.: 3663 Cov.: 33 AF XY: 0.211 AC XY: 15689 AN XY: 74360

Gnomad4 AFR AF: 0.307

Gnomad4 AMR AF: 0.186

Gnomad4 ASJ AF: 0.124

Gnomad4 EAS AF: 0.191

Gnomad4 SAS AF: 0.122

Gnomad4 FIN AF: 0.245

Gnomad4 NFE AF: 0.163

Gnomad4 OTH AF: 0.176

Alfa AF: 0.166 Hom.: 3059

Bravo AF: 0.208

Asia WGS AF: 0.184 AC: 639 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.79
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9578484; hg19: chr13-23223090;