rs9584093

chr13-93224531-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XM_047429990.1(GPC6):c.-2202T>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.198 in 152,172 control chromosomes in the GnomAD database, including 3,041 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 0.20 (3041 hom., cov: 32)
• Consequence: GPC6 XM_047429990.1 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.559

Genes affected

GPC6 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.292 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GPC6	XM_047429990.1	c.-2202T>C		5_prime_UTR_variant	1/9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.198 AC: 30104 AN: 152054 Hom.: 3043 Cov.: 32

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.0967

Gnomad AMR AF: 0.247

Gnomad ASJ AF: 0.205

Gnomad EAS AF: 0.305

Gnomad SAS AF: 0.220

Gnomad FIN AF: 0.184

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.202

Gnomad OTH AF: 0.211

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

GnomAD4 genome AF: 0.198 AC: 30101 AN: 152172 Hom.: 3041 Cov.: 32 AF XY: 0.198 AC XY: 14767 AN XY: 74400

Gnomad4 AFR AF: 0.161

Gnomad4 AMR AF: 0.246

Gnomad4 ASJ AF: 0.205

Gnomad4 EAS AF: 0.304

Gnomad4 SAS AF: 0.218

Gnomad4 FIN AF: 0.184

Gnomad4 NFE AF: 0.202

Gnomad4 OTH AF: 0.210

Alfa AF: 0.207 Hom.: 6842

Bravo AF: 0.203

Asia WGS AF: 0.243 AC: 847 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
Cadd	Benign	0.42
Dann	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9584093; hg19: chr13-93876784;