rs6494367

chr15-62923452-T-Cchr15-62923452-T-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 0.259 in 152,134 control chromosomes in the GnomAD database, including 5,808 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 0.26 (5808 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.505

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.475 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: 0.259 AC: 39356 AN: 152016 Hom.: 5793 Cov.: 33

Gnomad AFR AF: 0.355

Gnomad AMI AF: 0.182

Gnomad AMR AF: 0.322

Gnomad ASJ AF: 0.217

Gnomad EAS AF: 0.491

Gnomad SAS AF: 0.314

Gnomad FIN AF: 0.160

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.183

Gnomad OTH AF: 0.265

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

GnomAD4 genome AF: 0.259 AC: 39398 AN: 152134 Hom.: 5808 Cov.: 33 AF XY: 0.260 AC XY: 19370 AN XY: 74378

Gnomad4 AFR AF: 0.355

Gnomad4 AMR AF: 0.323

Gnomad4 ASJ AF: 0.217

Gnomad4 EAS AF: 0.491

Gnomad4 SAS AF: 0.313

Gnomad4 FIN AF: 0.160

Gnomad4 NFE AF: 0.183

Gnomad4 OTH AF: 0.268

Alfa AF: 0.206 Hom.: 3562

Bravo AF: 0.278

Asia WGS AF: 0.419 AC: 1456 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	1.3
Dann	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6494367; hg19: chr15-63215651;