rs2453533

chr15-45349027-C-Achr15-45349027-C-Gchr15-45349027-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 0.561 in 151,904 control chromosomes in the GnomAD database, including 27,391 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 0.56 (27391 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.886 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: 0.561 AC: 85099 AN: 151786 Hom.: 27336 Cov.: 31

Gnomad AFR AF: 0.843

Gnomad AMI AF: 0.235

Gnomad AMR AF: 0.620

Gnomad ASJ AF: 0.534

Gnomad EAS AF: 0.908

Gnomad SAS AF: 0.595

Gnomad FIN AF: 0.410

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.376

Gnomad OTH AF: 0.557

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

GnomAD4 genome AF: 0.561 AC: 85217 AN: 151904 Hom.: 27391 Cov.: 31 AF XY: 0.568 AC XY: 42128 AN XY: 74200

Gnomad4 AFR AF: 0.843

Gnomad4 AMR AF: 0.621

Gnomad4 ASJ AF: 0.534

Gnomad4 EAS AF: 0.908

Gnomad4 SAS AF: 0.593

Gnomad4 FIN AF: 0.410

Gnomad4 NFE AF: 0.376

Gnomad4 OTH AF: 0.561

Alfa AF: 0.436 Hom.: 18811

Bravo AF: 0.592

Asia WGS AF: 0.736 AC: 2558 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	0.56
Dann	Benign	0.15

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2453533; hg19: chr15-45641225;