rs17702471

Positions:

• chr13-93224864-A-G

Variant summary

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

The XM_047429990.1(GPC6):​c.-1869A>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.163 in 152,174 control chromosomes in the GnomAD database, including 2,328 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 0.16 (2328 hom., cov: 33)
• Consequence: GPC6 XM_047429990.1 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.252

Genes affected

GPC6 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.208 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GPC6	XM_047429990.1	c.-1869A>G		5_prime_UTR_variant	1/9		XP_047285946.1

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.163 AC: 24713 AN: 152056 Hom.: 2316 Cov.: 33

Gnomad AFR AF: 0.0789

Gnomad AMI AF: 0.0757

Gnomad AMR AF: 0.209

Gnomad ASJ AF: 0.156

Gnomad EAS AF: 0.0829

Gnomad SAS AF: 0.152

Gnomad FIN AF: 0.165

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.211

Gnomad OTH AF: 0.174

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

GnomAD4 genome AF: 0.163 AC: 24748 AN: 152174 Hom.: 2328 Cov.: 33 AF XY: 0.161 AC XY: 11972 AN XY: 74392

Gnomad4 AFR AF: 0.0789

Gnomad4 AMR AF: 0.209

Gnomad4 ASJ AF: 0.156

Gnomad4 EAS AF: 0.0826

Gnomad4 SAS AF: 0.153

Gnomad4 FIN AF: 0.165

Gnomad4 NFE AF: 0.211

Gnomad4 OTH AF: 0.179

Alfa AF: 0.203 Hom.: 4256

Bravo AF: 0.162

Asia WGS AF: 0.163 AC: 566 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	6.2
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17702471; hg19: chr13-93877117;