rs9301839

Positions:

• chr13-92845062-C-T

Variant summary

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

The NM_004466.6(GPC5):​c.1562-21220C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.135 in 151,786 control chromosomes in the GnomAD database, including 1,529 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 0.14 (1529 hom., cov: 32)
• Consequence: GPC5 NM_004466.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0230

Genes affected

GPC5 (HGNC:4453): (glypican 5) Cell surface heparan sulfate proteoglycans are composed of a membrane-associated protein core substituted with a variable number of heparan sulfate chains. Members of the glypican-related integral membrane proteoglycan family (GRIPS) contain a core protein anchored to the cytoplasmic membrane via a glycosyl phosphatidylinositol linkage. These proteins may play a role in the control of cell division and growth regulation. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.187 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GPC5	NM_004466.6	c.1562-21220C>T		intron_variant		ENST00000377067.9	NP_004457.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GPC5	ENST00000377067.9	c.1562-21220C>T		intron_variant		1	NM_004466.6	ENSP00000366267	P1

Frequencies

GnomAD3 genomes AF: 0.135 AC: 20521 AN: 151666 Hom.: 1525 Cov.: 32

Gnomad AFR AF: 0.191

Gnomad AMI AF: 0.0406

Gnomad AMR AF: 0.104

Gnomad ASJ AF: 0.172

Gnomad EAS AF: 0.00406

Gnomad SAS AF: 0.0702

Gnomad FIN AF: 0.144

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.121

Gnomad OTH AF: 0.140

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

GnomAD4 genome AF: 0.135 AC: 20539 AN: 151786 Hom.: 1529 Cov.: 32 AF XY: 0.132 AC XY: 9809 AN XY: 74122

Gnomad4 AFR AF: 0.191

Gnomad4 AMR AF: 0.104

Gnomad4 ASJ AF: 0.172

Gnomad4 EAS AF: 0.00407

Gnomad4 SAS AF: 0.0702

Gnomad4 FIN AF: 0.144

Gnomad4 NFE AF: 0.121

Gnomad4 OTH AF: 0.139

Alfa AF: 0.120 Hom.: 1905

Bravo AF: 0.135

Asia WGS AF: 0.0600 AC: 211 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.5
DANN	Benign	0.75

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs9301839; hg19: chr13-93497315;