3-146265901-G-T

Position:

• chr3-146265901-G-T

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 0.691 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.425

Gnomad4 AMR AF: 0.787

Gnomad4 ASJ AF: 0.861

Gnomad4 EAS AF: 0.678

Gnomad4 SAS AF: 0.736

Gnomad4 FIN AF: 0.765

Gnomad4 NFE AF: 0.806

Gnomad4 OTH AF: 0.698

Alfa AF: 0.760 Hom.: 18665

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9289719; hg19: chr3-145983688;