rs1449866

Variant names:

• chr3-143157791-G-T
• rs1449866

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 0.2 in 152,116 control chromosomes in the GnomAD database, including 3,768 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 0.20 (3768 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.654

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.339 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: 0.200 AC: 30440 AN: 151998 Hom.: 3757 Cov.: 33

Gnomad AFR AF: 0.344

Gnomad AMI AF: 0.167

Gnomad AMR AF: 0.194

Gnomad ASJ AF: 0.104

Gnomad EAS AF: 0.188

Gnomad SAS AF: 0.272

Gnomad FIN AF: 0.118

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.128

Gnomad OTH AF: 0.191

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

GnomAD4 genome AF: 0.200 AC: 30487 AN: 152116 Hom.: 3768 Cov.: 33 AF XY: 0.200 AC XY: 14875 AN XY: 74394

Gnomad4 AFR AF: 0.344

Gnomad4 AMR AF: 0.195

Gnomad4 ASJ AF: 0.104

Gnomad4 EAS AF: 0.189

Gnomad4 SAS AF: 0.270

Gnomad4 FIN AF: 0.118

Gnomad4 NFE AF: 0.128

Gnomad4 OTH AF: 0.193

Alfa AF: 0.151 Hom.: 1533

Bravo AF: 0.214

Asia WGS AF: 0.255 AC: 888 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	15
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: rs1449866; hg19: chr3-142876633;