rs920029

Variant names:

• chr9-32583509-A-G
• rs920029

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 0.186 in 152,168 control chromosomes in the GnomAD database, including 2,804 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 0.19 (2804 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.425

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.257 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: 0.186 AC: 28310 AN: 152050 Hom.: 2794 Cov.: 32

Gnomad AFR AF: 0.261

Gnomad AMI AF: 0.0824

Gnomad AMR AF: 0.164

Gnomad ASJ AF: 0.245

Gnomad EAS AF: 0.0919

Gnomad SAS AF: 0.165

Gnomad FIN AF: 0.187

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.154

Gnomad OTH AF: 0.172

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

GnomAD4 genome AF: 0.186 AC: 28341 AN: 152168 Hom.: 2804 Cov.: 32 AF XY: 0.184 AC XY: 13666 AN XY: 74392

Gnomad4 AFR AF: 0.261

Gnomad4 AMR AF: 0.164

Gnomad4 ASJ AF: 0.245

Gnomad4 EAS AF: 0.0923

Gnomad4 SAS AF: 0.166

Gnomad4 FIN AF: 0.187

Gnomad4 NFE AF: 0.154

Gnomad4 OTH AF: 0.170

Alfa AF: 0.168 Hom.: 1285

Bravo AF: 0.188

Asia WGS AF: 0.120 AC: 415 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	6.3
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs920029; hg19: chr9-32583507;