rs9825291

chr3-152787516-C-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 0.582 in 152,044 control chromosomes in the GnomAD database, including 27,427 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 0.58 (27427 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.05

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.725 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: 0.582 AC: 88446 AN: 151928 Hom.: 27417 Cov.: 32

Gnomad AFR AF: 0.344

Gnomad AMI AF: 0.642

Gnomad AMR AF: 0.684

Gnomad ASJ AF: 0.666

Gnomad EAS AF: 0.744

Gnomad SAS AF: 0.730

Gnomad FIN AF: 0.637

Gnomad MID AF: 0.620

Gnomad NFE AF: 0.667

Gnomad OTH AF: 0.595

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

GnomAD4 genome AF: 0.582 AC: 88473 AN: 152044 Hom.: 27427 Cov.: 32 AF XY: 0.585 AC XY: 43512 AN XY: 74328

Gnomad4 AFR AF: 0.344

Gnomad4 AMR AF: 0.684

Gnomad4 ASJ AF: 0.666

Gnomad4 EAS AF: 0.744

Gnomad4 SAS AF: 0.730

Gnomad4 FIN AF: 0.637

Gnomad4 NFE AF: 0.667

Gnomad4 OTH AF: 0.595

Alfa AF: 0.656 Hom.: 66488

Bravo AF: 0.570

Asia WGS AF: 0.721 AC: 2510 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	1.4
Dann	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9825291; hg19: chr3-152505305;