rs6494367

Variant names:

• chr15-62923452-T-C
• rs6494367

Your query was ambiguous. Multiple possible variants found:

• chr15-62923452-T-C
• chr15-62923452-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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;