rs7496492

Variant names:

• chr15-54952452-A-G
• rs7496492

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;