rs7328464

Variant names:

• chr13-91849410-C-T
• rs7328464
• NM_004466.6:c.1281-58527C>T

Variant summary

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

The NM_004466.6(GPC5):​c.1281-58527C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.134 in 152,118 control chromosomes in the GnomAD database, including 1,502 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 0.13 (1502 hom., cov: 32)
• Consequence: GPC5 NM_004466.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.92
• Publications: 7 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.188 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GPC5	NM_004466.6	c.1281-58527C>T		intron_variant	Intron 5 of 7	ENST00000377067.9	NP_004457.1
GPC5	XM_017020435.3	c.1281-58527C>T		intron_variant	Intron 5 of 7		XP_016875924.1
GPC5	XM_011521054.4	c.1281-58527C>T		intron_variant	Intron 5 of 6		XP_011519356.1
GPC5	XM_017020437.2	c.*26-58527C>T		intron_variant	Intron 6 of 6		XP_016875926.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GPC5	ENST00000377067.9	c.1281-58527C>T		intron_variant	Intron 5 of 7	1	NM_004466.6	ENSP00000366267.3

Frequencies

GnomAD3 genomes AF: 0.134 AC: 20324 AN: 152000 Hom.: 1499 Cov.: 32

Gnomad AFR AF: 0.192

Gnomad AMI AF: 0.191

Gnomad AMR AF: 0.0836

Gnomad ASJ AF: 0.0557

Gnomad EAS AF: 0.0874

Gnomad SAS AF: 0.0557

Gnomad FIN AF: 0.150

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.120

Gnomad OTH AF: 0.121

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

GnomAD4 genome AF: 0.134 AC: 20345 AN: 152118 Hom.: 1502 Cov.: 32 AF XY: 0.132 AC XY: 9810 AN XY: 74378

African (AFR) AF: 0.192 AC: 7959 AN: 41494

American (AMR) AF: 0.0835 AC: 1274 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.0557 AC: 193 AN: 3466

East Asian (EAS) AF: 0.0876 AC: 453 AN: 5172

South Asian (SAS) AF: 0.0554 AC: 267 AN: 4822

European-Finnish (FIN) AF: 0.150 AC: 1591 AN: 10582

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.120 AC: 8167 AN: 67998

Other (OTH) AF: 0.119 AC: 252 AN: 2112

Alfa AF: 0.120 Hom.: 3811

Bravo AF: 0.130

Asia WGS AF: 0.0690 AC: 240 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.042
DANN	Benign	0.44
PhyloP100		-3.9
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: rs7328464; hg19: chr13-92501664;