rs9290452

chr3-172844744-G-T

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 0.125 in 152,180 control chromosomes in the GnomAD database, including 1,875 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 0.12 (1875 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.172

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.258 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.125 AC: 18945 AN: 152062 Hom.: 1873 Cov.: 33

Gnomad AFR AF: 0.262

Gnomad AMI AF: 0.0471

Gnomad AMR AF: 0.0854

Gnomad ASJ AF: 0.134

Gnomad EAS AF: 0.106

Gnomad SAS AF: 0.217

Gnomad FIN AF: 0.0234

Gnomad MID AF: 0.0955

Gnomad NFE AF: 0.0610

Gnomad OTH AF: 0.122

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

GnomAD4 genome AF: 0.125 AC: 18975 AN: 152180 Hom.: 1875 Cov.: 33 AF XY: 0.124 AC XY: 9209 AN XY: 74408

Gnomad4 AFR AF: 0.262

Gnomad4 AMR AF: 0.0856

Gnomad4 ASJ AF: 0.134

Gnomad4 EAS AF: 0.106

Gnomad4 SAS AF: 0.217

Gnomad4 FIN AF: 0.0234

Gnomad4 NFE AF: 0.0610

Gnomad4 OTH AF: 0.122

Alfa AF: 0.0893 Hom.: 488

Bravo AF: 0.133

Asia WGS AF: 0.181 AC: 631 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	1.4
Dann	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9290452; hg19: chr3-172562534;