rs2863389

Variant names:

• chr3-166431104-C-T
• rs2863389

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 0.171 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
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.194 AC: 8049 AN: 41412

American (AMR) AF: 0.211 AC: 3214 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.164 AC: 567 AN: 3464

East Asian (EAS) AF: 0.0481 AC: 249 AN: 5178

South Asian (SAS) AF: 0.130 AC: 625 AN: 4818

European-Finnish (FIN) AF: 0.204 AC: 2154 AN: 10548

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.154 AC: 10449 AN: 67756

Other (OTH) AF: 0.195 AC: 410 AN: 2106

Alfa AF: 0.159 Hom.: 6617

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
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs2863389; hg19: chr3-166148892;