rs2863389

Variant names:

• chr3-166431104-C-T
• rs2863389

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 0.171 in 151,728 control chromosomes in the GnomAD database, including 2,218 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 0.17 (2218 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.187

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.55).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.205 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: 0.171 AC: 25890 AN: 151610 Hom.: 2211 Cov.: 32

Gnomad AFR AF: 0.195

Gnomad AMI AF: 0.122

Gnomad AMR AF: 0.210

Gnomad ASJ AF: 0.164

Gnomad EAS AF: 0.0482

Gnomad SAS AF: 0.130

Gnomad FIN AF: 0.204

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.154

Gnomad OTH AF: 0.197

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

GnomAD4 genome AF: 0.171 AC: 25908 AN: 151728 Hom.: 2218 Cov.: 32 AF XY: 0.172 AC XY: 12745 AN XY: 74148

Gnomad4 AFR AF: 0.194

Gnomad4 AMR AF: 0.211

Gnomad4 ASJ AF: 0.164

Gnomad4 EAS AF: 0.0481

Gnomad4 SAS AF: 0.130

Gnomad4 FIN AF: 0.204

Gnomad4 NFE AF: 0.154

Gnomad4 OTH AF: 0.195

Alfa AF: 0.161 Hom.: 2772

Bravo AF: 0.174

Asia WGS AF: 0.104 AC: 361 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.55
CADD	Benign	9.2
DANN	Benign	0.94

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2863389; hg19: chr3-166148892;