chr3-146673587-T-C

Position:

• chr3-146673587-T-C

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 0.836 in 151,920 control chromosomes in the GnomAD database, including 53,450 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 0.84 (53450 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.40

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.854 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.836 AC: 126957 AN: 151802 Hom.: 53406 Cov.: 31

Gnomad AFR AF: 0.836

Gnomad AMI AF: 0.825

Gnomad AMR AF: 0.808

Gnomad ASJ AF: 0.897

Gnomad EAS AF: 0.522

Gnomad SAS AF: 0.828

Gnomad FIN AF: 0.866

Gnomad MID AF: 0.896

Gnomad NFE AF: 0.860

Gnomad OTH AF: 0.831

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

GnomAD4 genome AF: 0.836 AC: 127058 AN: 151920 Hom.: 53450 Cov.: 31 AF XY: 0.833 AC XY: 61871 AN XY: 74242

Gnomad4 AFR AF: 0.836

Gnomad4 AMR AF: 0.808

Gnomad4 ASJ AF: 0.897

Gnomad4 EAS AF: 0.521

Gnomad4 SAS AF: 0.828

Gnomad4 FIN AF: 0.866

Gnomad4 NFE AF: 0.860

Gnomad4 OTH AF: 0.830

Alfa AF: 0.855 Hom.: 51978

Bravo AF: 0.833

Asia WGS AF: 0.724 AC: 2503 AN: 3456

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.35
DANN	Benign	0.22

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2868452; hg19: chr3-146391374;