rs2400405

Variant names:

• chr5-101401193-G-T
• rs2400405

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 0.125 in 149,726 control chromosomes in the GnomAD database, including 2,585 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 0.13 (2585 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.323

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.326 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: 0.125 AC: 18696 AN: 149608 Hom.: 2577 Cov.: 28

Gnomad AFR AF: 0.331

Gnomad AMI AF: 0.0143

Gnomad AMR AF: 0.185

Gnomad ASJ AF: 0.0412

Gnomad EAS AF: 0.0514

Gnomad SAS AF: 0.0489

Gnomad FIN AF: 0.00564

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0238

Gnomad OTH AF: 0.101

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

GnomAD4 genome AF: 0.125 AC: 18738 AN: 149726 Hom.: 2585 Cov.: 28 AF XY: 0.124 AC XY: 9028 AN XY: 72990

Gnomad4 AFR AF: 0.331

Gnomad4 AMR AF: 0.185

Gnomad4 ASJ AF: 0.0412

Gnomad4 EAS AF: 0.0511

Gnomad4 SAS AF: 0.0497

Gnomad4 FIN AF: 0.00564

Gnomad4 NFE AF: 0.0238

Gnomad4 OTH AF: 0.0999

Alfa AF: 0.0879 Hom.: 212

Bravo AF: 0.148

Asia WGS AF: 0.0790 AC: 276 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.63
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2400405; hg19: chr5-100736897;