3-146265901-G-T

Variant names:

• chr3-146265901-G-T
• rs9289719

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 0.691 in 151,766 control chromosomes in the GnomAD database, including 38,285 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 0.69 (38285 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.193
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.8 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: 0.691 AC: 104774 AN: 151646 Hom.: 38268 Cov.: 30

Gnomad AFR AF: 0.425

Gnomad AMI AF: 0.873

Gnomad AMR AF: 0.786

Gnomad ASJ AF: 0.861

Gnomad EAS AF: 0.678

Gnomad SAS AF: 0.736

Gnomad FIN AF: 0.765

Gnomad MID AF: 0.702

Gnomad NFE AF: 0.806

Gnomad OTH AF: 0.702

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

GnomAD4 genome AF: 0.691 AC: 104823 AN: 151766 Hom.: 38285 Cov.: 30 AF XY: 0.690 AC XY: 51146 AN XY: 74160

African (AFR) AF: 0.425 AC: 17583 AN: 41374

American (AMR) AF: 0.787 AC: 11971 AN: 15216

Ashkenazi Jewish (ASJ) AF: 0.861 AC: 2988 AN: 3470

East Asian (EAS) AF: 0.678 AC: 3495 AN: 5152

South Asian (SAS) AF: 0.736 AC: 3537 AN: 4808

European-Finnish (FIN) AF: 0.765 AC: 8080 AN: 10568

Middle Eastern (MID) AF: 0.716 AC: 209 AN: 292

European-Non Finnish (NFE) AF: 0.806 AC: 54691 AN: 67864

Other (OTH) AF: 0.698 AC: 1473 AN: 2110

Alfa AF: 0.770 Hom.: 26680

Bravo AF: 0.681

Asia WGS AF: 0.655 AC: 2282 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	5.9
DANN	Benign	0.71
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs9289719; hg19: chr3-145983688;