NM_004466.6:c.1562-154775G>T

Variant names:

• chr13-92711507-G-T
• rs9523787
• NM_004466.6:c.1562-154775G>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.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
• Publications: 5 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]

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

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 (NFE) allele frequency at 95% confidence interval = 0.205 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GPC5	NM_004466.6	c.1562-154775G>T		intron_variant	Intron 7 of 7	ENST00000377067.9	NP_004457.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GPC5	ENST00000377067.9	c.1562-154775G>T		intron_variant	Intron 7 of 7	1	NM_004466.6	ENSP00000366267.3
GPC5-AS1	ENST00000419288.1	n.82-1934C>A		intron_variant	Intron 1 of 3	3
GPC5-AS1	ENST00000451897.5	n.69-1934C>A		intron_variant	Intron 1 of 3	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

African (AFR) AF: 0.0502 AC: 2083 AN: 41490

American (AMR) AF: 0.158 AC: 2404 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.175 AC: 607 AN: 3468

East Asian (EAS) AF: 0.0861 AC: 445 AN: 5166

South Asian (SAS) AF: 0.105 AC: 509 AN: 4826

European-Finnish (FIN) AF: 0.135 AC: 1425 AN: 10564

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.208 AC: 14107 AN: 67912

Other (OTH) AF: 0.183 AC: 386 AN: 2110

Alfa AF: 0.168 Hom.: 424

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
PhyloP100		-0.29
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: rs9523787; hg19: chr13-93363760;