13-92670893-T-C

Variant names:

• chr13-92670893-T-C
• rs17267292
• NM_004466.6:c.1562-195389T>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.1562-195389T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.221 in 152,072 control chromosomes in the GnomAD database, including 4,382 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 0.22 (4382 hom., cov: 32)
• Consequence: GPC5 NM_004466.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.617
• Publications: 16 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]

ENSG00000287159 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.348 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GPC5	NM_004466.6	MANE Select	c.1562-195389T>C		intron	N/A	NP_004457.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GPC5	ENST00000377067.9	TSL:1 MANE Select	c.1562-195389T>C		intron	N/A	ENSP00000366267.3
	ENSG00000287159	ENST00000662499.2		n.230+6625A>G		intron	N/A
	ENSG00000287159	ENST00000756063.1		n.140+6625A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.221 AC: 33609 AN: 151954 Hom.: 4373 Cov.: 32

Gnomad AFR AF: 0.0948

Gnomad AMI AF: 0.271

Gnomad AMR AF: 0.198

Gnomad ASJ AF: 0.257

Gnomad EAS AF: 0.0925

Gnomad SAS AF: 0.359

Gnomad FIN AF: 0.336

Gnomad MID AF: 0.322

Gnomad NFE AF: 0.283

Gnomad OTH AF: 0.220

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

GnomAD4 genome AF: 0.221 AC: 33635 AN: 152072 Hom.: 4382 Cov.: 32 AF XY: 0.224 AC XY: 16669 AN XY: 74330

African (AFR) AF: 0.0947 AC: 3936 AN: 41542

American (AMR) AF: 0.197 AC: 3011 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.257 AC: 893 AN: 3470

East Asian (EAS) AF: 0.0925 AC: 477 AN: 5158

South Asian (SAS) AF: 0.362 AC: 1746 AN: 4822

European-Finnish (FIN) AF: 0.336 AC: 3551 AN: 10566

Middle Eastern (MID) AF: 0.322 AC: 94 AN: 292

European-Non Finnish (NFE) AF: 0.283 AC: 19208 AN: 67956

Other (OTH) AF: 0.224 AC: 472 AN: 2110

Alfa AF: 0.255 Hom.: 3778

Bravo AF: 0.200

Asia WGS AF: 0.206 AC: 716 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.5
DANN	Benign	0.50
PhyloP100		-0.62
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: rs17267292; hg19: chr13-93323146;