rs7496492

Positions:

• chr15-54952452-A-G

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 0.0639 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	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

Gnomad4 AFR AF: 0.206

Gnomad4 AMR AF: 0.0294

Gnomad4 ASJ AF: 0.0265

Gnomad4 EAS AF: 0.0121

Gnomad4 SAS AF: 0.00644

Gnomad4 FIN AF: 0.00284

Gnomad4 NFE AF: 0.00605

Gnomad4 OTH AF: 0.0484

Alfa AF: 0.0445 Hom.: 84

Bravo AF: 0.0721

Asia WGS AF: 0.0510 AC: 176 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7496492; hg19: chr15-55244650;