rs10492503

Variant names:

• chr13-92232844-T-A
• rs10492503
• NM_004466.6:c.1561+87855T>A

Variant summary

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

The NM_004466.6(GPC5):​c.1561+87855T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.352 in 152,086 control chromosomes in the GnomAD database, including 9,866 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 0.35 (9866 hom., cov: 32)
• Consequence: GPC5 NM_004466.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0530
• Publications: 9 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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.454 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GPC5	NM_004466.6	c.1561+87855T>A		intron_variant	Intron 7 of 7	ENST00000377067.9	NP_004457.1
GPC5	XM_017020435.3	c.1561+87855T>A		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.1561+87855T>A		intron_variant	Intron 7 of 7	1	NM_004466.6	ENSP00000366267.3

Frequencies

GnomAD3 genomes AF: 0.352 AC: 53420 AN: 151968 Hom.: 9850 Cov.: 32

Gnomad AFR AF: 0.460

Gnomad AMI AF: 0.239

Gnomad AMR AF: 0.332

Gnomad ASJ AF: 0.278

Gnomad EAS AF: 0.139

Gnomad SAS AF: 0.238

Gnomad FIN AF: 0.283

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.331

Gnomad OTH AF: 0.334

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

GnomAD4 genome AF: 0.352 AC: 53477 AN: 152086 Hom.: 9866 Cov.: 32 AF XY: 0.346 AC XY: 25731 AN XY: 74326

African (AFR) AF: 0.460 AC: 19074 AN: 41490

American (AMR) AF: 0.332 AC: 5075 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.278 AC: 964 AN: 3470

East Asian (EAS) AF: 0.139 AC: 721 AN: 5178

South Asian (SAS) AF: 0.239 AC: 1151 AN: 4824

European-Finnish (FIN) AF: 0.283 AC: 2988 AN: 10564

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.331 AC: 22492 AN: 67962

Other (OTH) AF: 0.334 AC: 706 AN: 2114

Alfa AF: 0.353 Hom.: 1183

Bravo AF: 0.361

Asia WGS AF: 0.229 AC: 793 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.1
DANN	Benign	0.33
PhyloP100		0.053
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: rs10492503; hg19: chr13-92885097;