rs1399552

Variant names:

• chr3-80499686-A-T
• rs1399552

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 0.055 in 152,190 control chromosomes in the GnomAD database, including 436 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 0.055 (436 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.508

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.136 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: 0.0549 AC: 8342 AN: 152074 Hom.: 433 Cov.: 33

Gnomad AFR AF: 0.139

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0343

Gnomad ASJ AF: 0.0548

Gnomad EAS AF: 0.000386

Gnomad SAS AF: 0.0641

Gnomad FIN AF: 0.0171

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0186

Gnomad OTH AF: 0.0497

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

GnomAD4 genome AF: 0.0550 AC: 8369 AN: 152190 Hom.: 436 Cov.: 33 AF XY: 0.0544 AC XY: 4051 AN XY: 74416

Gnomad4 AFR AF: 0.139

Gnomad4 AMR AF: 0.0343

Gnomad4 ASJ AF: 0.0548

Gnomad4 EAS AF: 0.000387

Gnomad4 SAS AF: 0.0648

Gnomad4 FIN AF: 0.0171

Gnomad4 NFE AF: 0.0186

Gnomad4 OTH AF: 0.0492

Alfa AF: 0.0376 Hom.: 27

Bravo AF: 0.0580

Asia WGS AF: 0.0320 AC: 111 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.11
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1399552; hg19: chr3-80548836;