rs9833265

Variant names:

• chr3-145291065-G-A
• rs9833265

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.0372 AC: 1543 AN: 41534

American (AMR) AF: 0.103 AC: 1582 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0770 AC: 267 AN: 3468

East Asian (EAS) AF: 0.0455 AC: 235 AN: 5166

South Asian (SAS) AF: 0.0653 AC: 315 AN: 4824

European-Finnish (FIN) AF: 0.0756 AC: 799 AN: 10570

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.0787 AC: 5353 AN: 68004

Other (OTH) AF: 0.0708 AC: 149 AN: 2106

Alfa AF: 0.0711 Hom.: 55

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
PhyloP100		-0.39

Splicing

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

Other links and lift over

dbSNP: rs9833265; hg19: chr3-145008852;