chr9-32583509-A-G

Variant names:

• chr9-32583509-A-G
• rs920029

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 0.186 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
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.261 AC: 10811 AN: 41478

American (AMR) AF: 0.164 AC: 2515 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.245 AC: 849 AN: 3466

East Asian (EAS) AF: 0.0923 AC: 479 AN: 5188

South Asian (SAS) AF: 0.166 AC: 800 AN: 4824

European-Finnish (FIN) AF: 0.187 AC: 1974 AN: 10584

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.154 AC: 10444 AN: 68012

Other (OTH) AF: 0.170 AC: 359 AN: 2114

Alfa AF: 0.168 Hom.: 1812

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
PhyloP100		0.42

Splicing

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

Other links and lift over

dbSNP: rs920029; hg19: chr9-32583507;