rs9832314

chr3-72468889-A-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.0634 in 152,306 control chromosomes in the GnomAD database, including 467 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 0.063 (467 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.94

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.27).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.193 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: 0.0634 AC: 9652 AN: 152188 Hom.: 464 Cov.: 32

Gnomad AFR AF: 0.0435

Gnomad AMI AF: 0.0485

Gnomad AMR AF: 0.0607

Gnomad ASJ AF: 0.0291

Gnomad EAS AF: 0.202

Gnomad SAS AF: 0.143

Gnomad FIN AF: 0.115

Gnomad MID AF: 0.0223

Gnomad NFE AF: 0.0541

Gnomad OTH AF: 0.0630

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

GnomAD4 genome AF: 0.0634 AC: 9662 AN: 152306 Hom.: 467 Cov.: 32 AF XY: 0.0688 AC XY: 5125 AN XY: 74466

Gnomad4 AFR AF: 0.0436

Gnomad4 AMR AF: 0.0604

Gnomad4 ASJ AF: 0.0291

Gnomad4 EAS AF: 0.203

Gnomad4 SAS AF: 0.142

Gnomad4 FIN AF: 0.115

Gnomad4 NFE AF: 0.0541

Gnomad4 OTH AF: 0.0643

Alfa AF: 0.0629 Hom.: 58

Bravo AF: 0.0567

Asia WGS AF: 0.189 AC: 658 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.27
Cadd	Benign	16
Dann	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9832314; hg19: chr3-72518040;