15-101499466-G-C

Position:

• chr15-101499466-G-C

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 0.369 in 151,872 control chromosomes in the GnomAD database, including 10,380 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 0.37 (10380 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.363

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.46 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.101499466G>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PCSK6	ENST00000557794.5	n.123+25614C>G		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.369 AC: 55935 AN: 151754 Hom.: 10379 Cov.: 31

Gnomad AFR AF: 0.353

Gnomad AMI AF: 0.484

Gnomad AMR AF: 0.423

Gnomad ASJ AF: 0.304

Gnomad EAS AF: 0.476

Gnomad SAS AF: 0.381

Gnomad FIN AF: 0.306

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.368

Gnomad OTH AF: 0.372

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

GnomAD4 genome AF: 0.369 AC: 55965 AN: 151872 Hom.: 10380 Cov.: 31 AF XY: 0.367 AC XY: 27252 AN XY: 74246

Gnomad4 AFR AF: 0.353

Gnomad4 AMR AF: 0.423

Gnomad4 ASJ AF: 0.304

Gnomad4 EAS AF: 0.475

Gnomad4 SAS AF: 0.381

Gnomad4 FIN AF: 0.306

Gnomad4 NFE AF: 0.368

Gnomad4 OTH AF: 0.370

Alfa AF: 0.221 Hom.: 508

Bravo AF: 0.379

Asia WGS AF: 0.385 AC: 1340 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.4
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8033863; hg19: chr15-102039669;