9-84215584-G-T

Variant names:

• chr9-84215584-G-T
• rs7874528

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 0.185 in 151,068 control chromosomes in the GnomAD database, including 4,819 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 0.18 (4819 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0930
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.453 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: 0.185 AC: 27870 AN: 150954 Hom.: 4804 Cov.: 31

Gnomad AFR AF: 0.459

Gnomad AMI AF: 0.216

Gnomad AMR AF: 0.147

Gnomad ASJ AF: 0.0580

Gnomad EAS AF: 0.00116

Gnomad SAS AF: 0.125

Gnomad FIN AF: 0.0997

Gnomad MID AF: 0.167

Gnomad NFE AF: 0.0663

Gnomad OTH AF: 0.149

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

GnomAD4 genome AF: 0.185 AC: 27914 AN: 151068 Hom.: 4819 Cov.: 31 AF XY: 0.184 AC XY: 13564 AN XY: 73740

African (AFR) AF: 0.459 AC: 18787 AN: 40944

American (AMR) AF: 0.147 AC: 2238 AN: 15196

Ashkenazi Jewish (ASJ) AF: 0.0580 AC: 201 AN: 3468

East Asian (EAS) AF: 0.00117 AC: 6 AN: 5142

South Asian (SAS) AF: 0.124 AC: 592 AN: 4788

European-Finnish (FIN) AF: 0.0997 AC: 1034 AN: 10368

Middle Eastern (MID) AF: 0.180 AC: 53 AN: 294

European-Non Finnish (NFE) AF: 0.0663 AC: 4499 AN: 67870

Other (OTH) AF: 0.147 AC: 308 AN: 2090

Alfa AF: 0.0906 Hom.: 1630

Bravo AF: 0.200

Asia WGS AF: 0.0800 AC: 277 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.1
DANN	Benign	0.69
PhyloP100		-0.093

Splicing

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

Other links and lift over

dbSNP: rs7874528; hg19: chr9-86830499;