9-84204575-C-G

Variant names:

• chr9-84204575-C-G
• rs2248048

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 0.425 in 151,924 control chromosomes in the GnomAD database, including 15,733 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 0.42 (15733 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.267

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.563 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: 0.425 AC: 64546 AN: 151806 Hom.: 15738 Cov.: 31

Gnomad AFR AF: 0.231

Gnomad AMI AF: 0.558

Gnomad AMR AF: 0.357

Gnomad ASJ AF: 0.570

Gnomad EAS AF: 0.0978

Gnomad SAS AF: 0.266

Gnomad FIN AF: 0.534

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.567

Gnomad OTH AF: 0.445

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

GnomAD4 genome AF: 0.425 AC: 64536 AN: 151924 Hom.: 15733 Cov.: 31 AF XY: 0.419 AC XY: 31091 AN XY: 74218

Gnomad4 AFR AF: 0.231

Gnomad4 AMR AF: 0.357

Gnomad4 ASJ AF: 0.570

Gnomad4 EAS AF: 0.0973

Gnomad4 SAS AF: 0.266

Gnomad4 FIN AF: 0.534

Gnomad4 NFE AF: 0.567

Gnomad4 OTH AF: 0.440

Alfa AF: 0.358 Hom.: 1055

Bravo AF: 0.405

Asia WGS AF: 0.172 AC: 603 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.89
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2248048; hg19: chr9-86819490;