rs9825310

Positions:

• chr3-32198627-G-A

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;