13-91896587-C-T

Variant names:

• chr13-91896587-C-T
• rs1330469
• NM_004466.6:c.1281-11350C>T

Variant summary

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

The NM_004466.6(GPC5):​c.1281-11350C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.397 in 151,792 control chromosomes in the GnomAD database, including 13,247 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 (13247 hom., cov: 30)
• Consequence: GPC5 NM_004466.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.413

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.628 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GPC5	NM_004466.6	c.1281-11350C>T		intron_variant	Intron 5 of 7	ENST00000377067.9	NP_004457.1
GPC5	XM_017020435.3	c.1281-11350C>T		intron_variant	Intron 5 of 7		XP_016875924.1
GPC5	XM_011521054.4	c.1281-11350C>T		intron_variant	Intron 5 of 6		XP_011519356.1
GPC5	XM_017020437.2	c.*26-11350C>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.1281-11350C>T		intron_variant	Intron 5 of 7	1	NM_004466.6	ENSP00000366267.3

Frequencies

GnomAD3 genomes AF: 0.397 AC: 60207 AN: 151674 Hom.: 13248 Cov.: 30

Gnomad AFR AF: 0.214

Gnomad AMI AF: 0.442

Gnomad AMR AF: 0.413

Gnomad ASJ AF: 0.551

Gnomad EAS AF: 0.606

Gnomad SAS AF: 0.647

Gnomad FIN AF: 0.376

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.464

Gnomad OTH AF: 0.431

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

GnomAD4 genome AF: 0.397 AC: 60221 AN: 151792 Hom.: 13247 Cov.: 30 AF XY: 0.402 AC XY: 29793 AN XY: 74150

Gnomad4 AFR AF: 0.214

Gnomad4 AMR AF: 0.413

Gnomad4 ASJ AF: 0.551

Gnomad4 EAS AF: 0.606

Gnomad4 SAS AF: 0.647

Gnomad4 FIN AF: 0.376

Gnomad4 NFE AF: 0.464

Gnomad4 OTH AF: 0.433

Alfa AF: 0.444 Hom.: 9536

Bravo AF: 0.388

Asia WGS AF: 0.568 AC: 1976 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.4
DANN	Benign	0.81

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: rs1330469; hg19: chr13-92548841;