rs6494306

Variant names:

• chr15-62102341-G-A
• rs6494306

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 9 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.397 AC: 16443 AN: 41432

American (AMR) AF: 0.244 AC: 3721 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.172 AC: 595 AN: 3468

East Asian (EAS) AF: 0.277 AC: 1430 AN: 5156

South Asian (SAS) AF: 0.207 AC: 994 AN: 4806

European-Finnish (FIN) AF: 0.333 AC: 3507 AN: 10540

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.219 AC: 14907 AN: 67948

Other (OTH) AF: 0.266 AC: 561 AN: 2106

Alfa AF: 0.244 Hom.: 1197

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
PhyloP100		-0.49

Splicing

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

Other links and lift over

dbSNP: rs6494306; hg19: chr15-62394540;