rs9523762

Variant names:

• chr13-92679633-G-A
• rs9523762
• NM_004466.6:c.1562-186649G>A

Your query was ambiguous. Multiple possible variants found:

• chr13-92679633-G-A
• chr13-92679633-G-C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_004466.6(GPC5):​c.1562-186649G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.396 in 151,696 control chromosomes in the GnomAD database, including 12,123 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 0.40 (12123 hom., cov: 32)
• Consequence: GPC5 NM_004466.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.56
• Publications: 28 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.5).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.497 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_004466.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GPC5	NM_004466.6	MANE Select	c.1562-186649G>A		intron	N/A	NP_004457.1	P78333

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GPC5	ENST00000377067.9	TSL:1 MANE Select	c.1562-186649G>A		intron	N/A	ENSP00000366267.3	P78333

Frequencies

GnomAD3 genomes AF: 0.396 AC: 60044 AN: 151576 Hom.: 12093 Cov.: 32

Gnomad AFR AF: 0.392

Gnomad AMI AF: 0.299

Gnomad AMR AF: 0.506

Gnomad ASJ AF: 0.353

Gnomad EAS AF: 0.509

Gnomad SAS AF: 0.432

Gnomad FIN AF: 0.397

Gnomad MID AF: 0.298

Gnomad NFE AF: 0.366

Gnomad OTH AF: 0.417

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

GnomAD4 genome AF: 0.396 AC: 60120 AN: 151696 Hom.: 12123 Cov.: 32 AF XY: 0.401 AC XY: 29686 AN XY: 74060

African (AFR) AF: 0.392 AC: 16219 AN: 41376

American (AMR) AF: 0.507 AC: 7708 AN: 15210

Ashkenazi Jewish (ASJ) AF: 0.353 AC: 1225 AN: 3470

East Asian (EAS) AF: 0.510 AC: 2621 AN: 5142

South Asian (SAS) AF: 0.434 AC: 2079 AN: 4794

European-Finnish (FIN) AF: 0.397 AC: 4156 AN: 10466

Middle Eastern (MID) AF: 0.297 AC: 86 AN: 290

European-Non Finnish (NFE) AF: 0.366 AC: 24879 AN: 67928

Other (OTH) AF: 0.415 AC: 875 AN: 2110

Alfa AF: 0.385 Hom.: 28589

Bravo AF: 0.411

Asia WGS AF: 0.464 AC: 1617 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.50
CADD	Benign	17
DANN	Benign	0.53
PhyloP100		1.6
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs9523762; hg19: chr13-93331886;