rs9833265

Variant names:

• chr3-145291065-G-A
• rs9833265

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 0.068 in 152,170 control chromosomes in the GnomAD database, including 378 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 0.068 (378 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.386

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0992 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: 0.0680 AC: 10347 AN: 152050 Hom.: 377 Cov.: 33

Gnomad AFR AF: 0.0371

Gnomad AMI AF: 0.0998

Gnomad AMR AF: 0.104

Gnomad ASJ AF: 0.0770

Gnomad EAS AF: 0.0452

Gnomad SAS AF: 0.0653

Gnomad FIN AF: 0.0756

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0787

Gnomad OTH AF: 0.0710

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

GnomAD4 genome AF: 0.0680 AC: 10354 AN: 152170 Hom.: 378 Cov.: 33 AF XY: 0.0684 AC XY: 5087 AN XY: 74392

Gnomad4 AFR AF: 0.0372

Gnomad4 AMR AF: 0.103

Gnomad4 ASJ AF: 0.0770

Gnomad4 EAS AF: 0.0455

Gnomad4 SAS AF: 0.0653

Gnomad4 FIN AF: 0.0756

Gnomad4 NFE AF: 0.0787

Gnomad4 OTH AF: 0.0708

Alfa AF: 0.0723 Hom.: 54

Bravo AF: 0.0708

Asia WGS AF: 0.0630 AC: 218 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.6
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9833265; hg19: chr3-145008852;