rs9832461

Variant names:

• chr3-39708102-A-G
• rs9832461

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 0.261 in 152,164 control chromosomes in the GnomAD database, including 5,506 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 0.26 (5506 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.578

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.357 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: 0.260 AC: 39596 AN: 152046 Hom.: 5484 Cov.: 32

Gnomad AFR AF: 0.361

Gnomad AMI AF: 0.175

Gnomad AMR AF: 0.215

Gnomad ASJ AF: 0.218

Gnomad EAS AF: 0.126

Gnomad SAS AF: 0.212

Gnomad FIN AF: 0.200

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.237

Gnomad OTH AF: 0.238

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

GnomAD4 genome AF: 0.261 AC: 39652 AN: 152164 Hom.: 5506 Cov.: 32 AF XY: 0.256 AC XY: 19060 AN XY: 74404

Gnomad4 AFR AF: 0.362

Gnomad4 AMR AF: 0.215

Gnomad4 ASJ AF: 0.218

Gnomad4 EAS AF: 0.126

Gnomad4 SAS AF: 0.212

Gnomad4 FIN AF: 0.200

Gnomad4 NFE AF: 0.237

Gnomad4 OTH AF: 0.236

Alfa AF: 0.234 Hom.: 8250

Bravo AF: 0.261

Asia WGS AF: 0.175 AC: 610 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.6
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9832461; hg19: chr3-39749593;