9-133278037-C-T

Variant names:

• chr9-133278037-C-T
• rs552148

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 0.256 in 152,006 control chromosomes in the GnomAD database, including 5,226 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 0.26 (5226 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.212

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (Cadd=7.344).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.37 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: 0.256 AC: 38833 AN: 151888 Hom.: 5222 Cov.: 32

Gnomad AFR AF: 0.248

Gnomad AMI AF: 0.0965

Gnomad AMR AF: 0.378

Gnomad ASJ AF: 0.276

Gnomad EAS AF: 0.286

Gnomad SAS AF: 0.216

Gnomad FIN AF: 0.195

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.244

Gnomad OTH AF: 0.251

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

GnomAD4 genome AF: 0.256 AC: 38852 AN: 152006 Hom.: 5226 Cov.: 32 AF XY: 0.256 AC XY: 19014 AN XY: 74288

Gnomad4 AFR AF: 0.247

Gnomad4 AMR AF: 0.378

Gnomad4 ASJ AF: 0.276

Gnomad4 EAS AF: 0.285

Gnomad4 SAS AF: 0.216

Gnomad4 FIN AF: 0.195

Gnomad4 NFE AF: 0.244

Gnomad4 OTH AF: 0.250

Alfa AF: 0.251 Hom.: 6896

Bravo AF: 0.274

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
CADD	Benign	7.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs552148; hg19: -;