rs1399754

Variant names:

• chr3-58233690-A-G
• rs1399754

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 0.755 in 152,088 control chromosomes in the GnomAD database, including 44,483 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 0.75 (44483 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.521
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.974 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: 0.754 AC: 114655 AN: 151970 Hom.: 44423 Cov.: 31

Gnomad AFR AF: 0.911

Gnomad AMI AF: 0.805

Gnomad AMR AF: 0.741

Gnomad ASJ AF: 0.643

Gnomad EAS AF: 0.997

Gnomad SAS AF: 0.825

Gnomad FIN AF: 0.694

Gnomad MID AF: 0.706

Gnomad NFE AF: 0.654

Gnomad OTH AF: 0.734

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

GnomAD4 genome AF: 0.755 AC: 114773 AN: 152088 Hom.: 44483 Cov.: 31 AF XY: 0.760 AC XY: 56531 AN XY: 74350

African (AFR) AF: 0.911 AC: 37803 AN: 41504

American (AMR) AF: 0.741 AC: 11311 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.643 AC: 2230 AN: 3468

East Asian (EAS) AF: 0.997 AC: 5161 AN: 5176

South Asian (SAS) AF: 0.824 AC: 3972 AN: 4822

European-Finnish (FIN) AF: 0.694 AC: 7324 AN: 10552

Middle Eastern (MID) AF: 0.714 AC: 210 AN: 294

European-Non Finnish (NFE) AF: 0.654 AC: 44472 AN: 67982

Other (OTH) AF: 0.737 AC: 1556 AN: 2112

Alfa AF: 0.726 Hom.: 5298

Bravo AF: 0.764

Asia WGS AF: 0.919 AC: 3199 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.3
DANN	Benign	0.71
PhyloP100		-0.52

Splicing

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

Other links and lift over

dbSNP: rs1399754; hg19: chr3-58219417;