rs7874528

Variant names:

• chr9-84215584-G-T
• rs7874528

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 0.185 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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.459

Gnomad4 AMR AF: 0.147

Gnomad4 ASJ AF: 0.0580

Gnomad4 EAS AF: 0.00117

Gnomad4 SAS AF: 0.124

Gnomad4 FIN AF: 0.0997

Gnomad4 NFE AF: 0.0663

Gnomad4 OTH AF: 0.147

Alfa AF: 0.0864 Hom.: 1272

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7874528; hg19: chr9-86830499;