3-146673587-T-C

Variant names:

• chr3-146673587-T-C
• rs2868452

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 0.836 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
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.836 AC: 34645 AN: 41424

American (AMR) AF: 0.808 AC: 12312 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.897 AC: 3114 AN: 3470

East Asian (EAS) AF: 0.521 AC: 2695 AN: 5168

South Asian (SAS) AF: 0.828 AC: 3991 AN: 4820

European-Finnish (FIN) AF: 0.866 AC: 9115 AN: 10530

Middle Eastern (MID) AF: 0.884 AC: 260 AN: 294

European-Non Finnish (NFE) AF: 0.860 AC: 58429 AN: 67958

Other (OTH) AF: 0.830 AC: 1746 AN: 2104

Alfa AF: 0.854 Hom.: 68434

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
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs2868452; hg19: chr3-146391374;