chr15-54952452-A-G

Variant names:

• chr15-54952452-A-G
• rs7496492

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 0.0639 in 151,744 control chromosomes in the GnomAD database, including 909 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 0.064 (909 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0810
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.202 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.0636 AC: 9644 AN: 151626 Hom.: 891 Cov.: 32

Gnomad AFR AF: 0.205

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.0295

Gnomad ASJ AF: 0.0265

Gnomad EAS AF: 0.0121

Gnomad SAS AF: 0.00665

Gnomad FIN AF: 0.00284

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.00605

Gnomad OTH AF: 0.0465

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

GnomAD4 genome AF: 0.0639 AC: 9703 AN: 151744 Hom.: 909 Cov.: 32 AF XY: 0.0617 AC XY: 4577 AN XY: 74142

African (AFR) AF: 0.206 AC: 8513 AN: 41362

American (AMR) AF: 0.0294 AC: 448 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.0265 AC: 92 AN: 3468

East Asian (EAS) AF: 0.0121 AC: 62 AN: 5116

South Asian (SAS) AF: 0.00644 AC: 31 AN: 4810

European-Finnish (FIN) AF: 0.00284 AC: 30 AN: 10548

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.00605 AC: 411 AN: 67896

Other (OTH) AF: 0.0484 AC: 102 AN: 2106

Alfa AF: 0.0496 Hom.: 98

Bravo AF: 0.0721

Asia WGS AF: 0.0510 AC: 176 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.2
DANN	Benign	0.69
PhyloP100		-0.081

Splicing

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

Other links and lift over

dbSNP: rs7496492; hg19: chr15-55244650;