rs2468513

chr5-36454029-C-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 0.0922 in 149,766 control chromosomes in the GnomAD database, including 787 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 0.092 (787 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.44

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.159 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: 0.0921 AC: 13781 AN: 149648 Hom.: 783 Cov.: 33

Gnomad AFR AF: 0.159

Gnomad AMI AF: 0.0199

Gnomad AMR AF: 0.0726

Gnomad ASJ AF: 0.0602

Gnomad EAS AF: 0.0375

Gnomad SAS AF: 0.170

Gnomad FIN AF: 0.0552

Gnomad MID AF: 0.0732

Gnomad NFE AF: 0.0625

Gnomad OTH AF: 0.0914

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

GnomAD4 genome AF: 0.0922 AC: 13804 AN: 149766 Hom.: 787 Cov.: 33 AF XY: 0.0930 AC XY: 6789 AN XY: 72978

Gnomad4 AFR AF: 0.159

Gnomad4 AMR AF: 0.0724

Gnomad4 ASJ AF: 0.0602

Gnomad4 EAS AF: 0.0376

Gnomad4 SAS AF: 0.169

Gnomad4 FIN AF: 0.0552

Gnomad4 NFE AF: 0.0625

Gnomad4 OTH AF: 0.0904

Alfa AF: 0.0761 Hom.: 73

Bravo AF: 0.0898

Asia WGS AF: 0.116 AC: 402 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.98
Dann	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2468513; hg19: chr5-36454131;