rs16946160

Variant names:

• chr13-91551559-G-A
• rs16946160
• NM_004466.6:c.325+102637G>A

Variant summary

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

The ENST00000377067.9(GPC5):​c.325+102637G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.129 in 151,966 control chromosomes in the GnomAD database, including 1,566 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 0.13 (1566 hom., cov: 32)
• Consequence: GPC5 ENST00000377067.9 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.365
• Publications: 14 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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.213 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000377067.9. 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.325+102637G>A		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.325+102637G>A		intron	N/A	ENSP00000366267.3

Frequencies

GnomAD3 genomes AF: 0.129 AC: 19544 AN: 151846 Hom.: 1567 Cov.: 32

Gnomad AFR AF: 0.217

Gnomad AMI AF: 0.127

Gnomad AMR AF: 0.181

Gnomad ASJ AF: 0.0946

Gnomad EAS AF: 0.206

Gnomad SAS AF: 0.0734

Gnomad FIN AF: 0.0541

Gnomad MID AF: 0.137

Gnomad NFE AF: 0.0744

Gnomad OTH AF: 0.136

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

GnomAD4 genome AF: 0.129 AC: 19566 AN: 151966 Hom.: 1566 Cov.: 32 AF XY: 0.129 AC XY: 9556 AN XY: 74272

African (AFR) AF: 0.217 AC: 8990 AN: 41438

American (AMR) AF: 0.181 AC: 2762 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.0946 AC: 328 AN: 3468

East Asian (EAS) AF: 0.206 AC: 1059 AN: 5148

South Asian (SAS) AF: 0.0728 AC: 351 AN: 4822

European-Finnish (FIN) AF: 0.0541 AC: 572 AN: 10582

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.0744 AC: 5058 AN: 67942

Other (OTH) AF: 0.136 AC: 288 AN: 2114

Alfa AF: 0.0915 Hom.: 3001

Bravo AF: 0.142

Asia WGS AF: 0.131 AC: 455 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.3
DANN	Benign	0.53
PhyloP100		-0.36
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: rs16946160; hg19: chr13-92203813;