rs2453533

Variant names:

• chr15-45349027-C-A
• rs2453533

Your query was ambiguous. Multiple possible variants found:

• chr15-45349027-C-A
• chr15-45349027-C-G
• chr15-45349027-C-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 40 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.843 AC: 34937 AN: 41454

American (AMR) AF: 0.621 AC: 9470 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.534 AC: 1853 AN: 3470

East Asian (EAS) AF: 0.908 AC: 4684 AN: 5158

South Asian (SAS) AF: 0.593 AC: 2847 AN: 4798

European-Finnish (FIN) AF: 0.410 AC: 4322 AN: 10530

Middle Eastern (MID) AF: 0.558 AC: 164 AN: 294

European-Non Finnish (NFE) AF: 0.376 AC: 25541 AN: 67922

Other (OTH) AF: 0.561 AC: 1185 AN: 2112

Alfa AF: 0.455 Hom.: 55012

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
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs2453533; hg19: chr15-45641225;