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. The variant received -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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.355 AC: 14712 AN: 41450

American (AMR) AF: 0.323 AC: 4932 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.217 AC: 755 AN: 3472

East Asian (EAS) AF: 0.491 AC: 2540 AN: 5176

South Asian (SAS) AF: 0.313 AC: 1510 AN: 4822

European-Finnish (FIN) AF: 0.160 AC: 1696 AN: 10598

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.183 AC: 12459 AN: 68014

Other (OTH) AF: 0.268 AC: 566 AN: 2114

Alfa AF: 0.215 Hom.: 5006

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
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs6494367; hg19: chr15-63215651;