rs1449866

chr3-143157791-G-T

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;