rs9523787

chr13-92711507-G-T

Variant summary

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

The NM_004466.6(GPC5):c.1562-154775G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.146 in 152,004 control chromosomes in the GnomAD database, including 1,996 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 0.15 (1996 hom., cov: 32)
• Consequence: GPC5 NM_004466.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.288

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]

GPC5-AS1 (HGNC:39886): (GPC5 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.205 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GPC5	NM_004466.6	c.1562-154775G>T		intron_variant		ENST00000377067.9
GPC5-AS1	NR_046520.1	n.82-1934C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GPC5	ENST00000377067.9	c.1562-154775G>T		intron_variant		1	NM_004466.6	P1
GPC5-AS1	ENST00000419288.1	n.82-1934C>A		intron_variant, non_coding_transcript_variant		3
GPC5-AS1	ENST00000451897.5	n.69-1934C>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.146 AC: 22237 AN: 151886 Hom.: 1997 Cov.: 32

Gnomad AFR AF: 0.0504

Gnomad AMI AF: 0.236

Gnomad AMR AF: 0.158

Gnomad ASJ AF: 0.175

Gnomad EAS AF: 0.0861

Gnomad SAS AF: 0.106

Gnomad FIN AF: 0.135

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.208

Gnomad OTH AF: 0.183

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

GnomAD4 genome AF: 0.146 AC: 22230 AN: 152004 Hom.: 1996 Cov.: 32 AF XY: 0.143 AC XY: 10618 AN XY: 74280

Gnomad4 AFR AF: 0.0502

Gnomad4 AMR AF: 0.158

Gnomad4 ASJ AF: 0.175

Gnomad4 EAS AF: 0.0861

Gnomad4 SAS AF: 0.105

Gnomad4 FIN AF: 0.135

Gnomad4 NFE AF: 0.208

Gnomad4 OTH AF: 0.183

Alfa AF: 0.171 Hom.: 422

Bravo AF: 0.144

Asia WGS AF: 0.0760 AC: 265 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.38
Dann	Benign	0.64

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: rs9523787; hg19: chr13-93363760;