chr13-92741242-C-T

Variant names:

• chr13-92741242-C-T
• rs9516129
• NM_004466.6:c.1562-125040C>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.1562-125040C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.255 in 150,444 control chromosomes in the GnomAD database, including 5,110 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 0.25 (5110 hom., cov: 27)
• Consequence: GPC5 NM_004466.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.627
• Publications: 1 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=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.477 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GPC5	NM_004466.6	c.1562-125040C>T		intron_variant	Intron 7 of 7	ENST00000377067.9	NP_004457.1
GPC5	XM_017020435.3	c.1562-8722C>T		intron_variant	Intron 7 of 7		XP_016875924.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GPC5	ENST00000377067.9	c.1562-125040C>T		intron_variant	Intron 7 of 7	1	NM_004466.6	ENSP00000366267.3

Frequencies

GnomAD3 genomes AF: 0.255 AC: 38280 AN: 150326 Hom.: 5112 Cov.: 27

Gnomad AFR AF: 0.246

Gnomad AMI AF: 0.256

Gnomad AMR AF: 0.265

Gnomad ASJ AF: 0.225

Gnomad EAS AF: 0.494

Gnomad SAS AF: 0.339

Gnomad FIN AF: 0.159

Gnomad MID AF: 0.217

Gnomad NFE AF: 0.250

Gnomad OTH AF: 0.275

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

GnomAD4 genome AF: 0.255 AC: 38293 AN: 150444 Hom.: 5110 Cov.: 27 AF XY: 0.256 AC XY: 18793 AN XY: 73406

African (AFR) AF: 0.246 AC: 10051 AN: 40938

American (AMR) AF: 0.264 AC: 3969 AN: 15020

Ashkenazi Jewish (ASJ) AF: 0.225 AC: 777 AN: 3458

East Asian (EAS) AF: 0.493 AC: 2448 AN: 4962

South Asian (SAS) AF: 0.337 AC: 1602 AN: 4758

European-Finnish (FIN) AF: 0.159 AC: 1647 AN: 10366

Middle Eastern (MID) AF: 0.209 AC: 61 AN: 292

European-Non Finnish (NFE) AF: 0.250 AC: 16921 AN: 67652

Other (OTH) AF: 0.280 AC: 585 AN: 2092

Alfa AF: 0.251 Hom.: 2568

Bravo AF: 0.260

Asia WGS AF: 0.419 AC: 1452 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.76
PhyloP100		-0.63
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: rs9516129; hg19: chr13-93393495;