rs9825310

Variant names:

• chr3-32198627-G-A
• rs9825310

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 0.392 in 152,134 control chromosomes in the GnomAD database, including 12,971 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 0.39 (12971 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.559

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.472 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: 0.392 AC: 59564 AN: 152016 Hom.: 12972 Cov.: 32

Gnomad AFR AF: 0.217

Gnomad AMI AF: 0.622

Gnomad AMR AF: 0.455

Gnomad ASJ AF: 0.405

Gnomad EAS AF: 0.207

Gnomad SAS AF: 0.348

Gnomad FIN AF: 0.528

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.476

Gnomad OTH AF: 0.388

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

GnomAD4 genome AF: 0.392 AC: 59582 AN: 152134 Hom.: 12971 Cov.: 32 AF XY: 0.396 AC XY: 29411 AN XY: 74360

Gnomad4 AFR AF: 0.217

Gnomad4 AMR AF: 0.455

Gnomad4 ASJ AF: 0.405

Gnomad4 EAS AF: 0.207

Gnomad4 SAS AF: 0.350

Gnomad4 FIN AF: 0.528

Gnomad4 NFE AF: 0.476

Gnomad4 OTH AF: 0.385

Alfa AF: 0.449 Hom.: 14728

Bravo AF: 0.378

Asia WGS AF: 0.266 AC: 928 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.33
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9825310; hg19: chr3-32240119;