rs2401798

Variant names:

• chr5-13384375-T-C
• rs2401798

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 0.212 in 152,110 control chromosomes in the GnomAD database, including 3,737 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 0.21 (3737 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.195

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.269 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: 0.212 AC: 32257 AN: 151992 Hom.: 3728 Cov.: 29

Gnomad AFR AF: 0.273

Gnomad AMI AF: 0.275

Gnomad AMR AF: 0.220

Gnomad ASJ AF: 0.141

Gnomad EAS AF: 0.115

Gnomad SAS AF: 0.155

Gnomad FIN AF: 0.231

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.185

Gnomad OTH AF: 0.212

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

GnomAD4 genome AF: 0.212 AC: 32300 AN: 152110 Hom.: 3737 Cov.: 29 AF XY: 0.214 AC XY: 15885 AN XY: 74380

Gnomad4 AFR AF: 0.273

Gnomad4 AMR AF: 0.220

Gnomad4 ASJ AF: 0.141

Gnomad4 EAS AF: 0.115

Gnomad4 SAS AF: 0.155

Gnomad4 FIN AF: 0.231

Gnomad4 NFE AF: 0.185

Gnomad4 OTH AF: 0.211

Alfa AF: 0.189 Hom.: 370

Bravo AF: 0.217

Asia WGS AF: 0.149 AC: 518 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	0.27
DANN	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2401798; hg19: chr5-13384487;