13-91520023-G-A

Variant names:

• chr13-91520023-G-A
• rs2351871
• NM_004466.6:c.325+71101G>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.325+71101G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.549 in 151,962 control chromosomes in the GnomAD database, including 27,392 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 0.55 (27392 hom., cov: 32)
• Consequence: GPC5 NM_004466.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0520
• Publications: 6 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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.717 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.325+71101G>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+71101G>A		intron	N/A	ENSP00000366267.3

Frequencies

GnomAD3 genomes AF: 0.549 AC: 83420 AN: 151844 Hom.: 27391 Cov.: 32

Gnomad AFR AF: 0.163

Gnomad AMI AF: 0.668

Gnomad AMR AF: 0.603

Gnomad ASJ AF: 0.715

Gnomad EAS AF: 0.707

Gnomad SAS AF: 0.547

Gnomad FIN AF: 0.725

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.723

Gnomad OTH AF: 0.565

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

GnomAD4 genome AF: 0.549 AC: 83424 AN: 151962 Hom.: 27392 Cov.: 32 AF XY: 0.550 AC XY: 40825 AN XY: 74278

African (AFR) AF: 0.162 AC: 6731 AN: 41436

American (AMR) AF: 0.603 AC: 9196 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.715 AC: 2482 AN: 3470

East Asian (EAS) AF: 0.706 AC: 3645 AN: 5160

South Asian (SAS) AF: 0.549 AC: 2646 AN: 4818

European-Finnish (FIN) AF: 0.725 AC: 7646 AN: 10552

Middle Eastern (MID) AF: 0.585 AC: 172 AN: 294

European-Non Finnish (NFE) AF: 0.723 AC: 49106 AN: 67958

Other (OTH) AF: 0.565 AC: 1192 AN: 2108

Alfa AF: 0.668 Hom.: 59250

Bravo AF: 0.527

Asia WGS AF: 0.605 AC: 2105 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.1
DANN	Benign	0.45
PhyloP100		-0.052
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: rs2351871; hg19: chr13-92172277;