rs6494306

Variant names:

• chr15-62102341-G-A
• rs6494306

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 0.279 in 151,934 control chromosomes in the GnomAD database, including 6,429 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 0.28 (6429 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.495

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.392 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: 0.279 AC: 42368 AN: 151816 Hom.: 6407 Cov.: 32

Gnomad AFR AF: 0.397

Gnomad AMI AF: 0.255

Gnomad AMR AF: 0.243

Gnomad ASJ AF: 0.172

Gnomad EAS AF: 0.277

Gnomad SAS AF: 0.206

Gnomad FIN AF: 0.333

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.219

Gnomad OTH AF: 0.263

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

GnomAD4 genome AF: 0.279 AC: 42442 AN: 151934 Hom.: 6429 Cov.: 32 AF XY: 0.282 AC XY: 20941 AN XY: 74256

Gnomad4 AFR AF: 0.397

Gnomad4 AMR AF: 0.244

Gnomad4 ASJ AF: 0.172

Gnomad4 EAS AF: 0.277

Gnomad4 SAS AF: 0.207

Gnomad4 FIN AF: 0.333

Gnomad4 NFE AF: 0.219

Gnomad4 OTH AF: 0.266

Alfa AF: 0.241 Hom.: 1133

Bravo AF: 0.277

Asia WGS AF: 0.290 AC: 1007 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.73
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6494306; hg19: chr15-62394540;