rs2352029

Variant names:

• chr13-91793001-A-C
• rs2352029
• NM_004466.6:c.1280+36581A>C

Your query was ambiguous. Multiple possible variants found:

• chr13-91793001-A-C
• chr13-91793001-A-G
• chr13-91793001-A-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.1280+36581A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.36 in 151,966 control chromosomes in the GnomAD database, including 11,152 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 0.36 (11152 hom., cov: 32)
• Consequence: GPC5 NM_004466.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.115
• Publications: 12 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.552 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GPC5	NM_004466.6	c.1280+36581A>C		intron_variant	Intron 5 of 7	ENST00000377067.9	NP_004457.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GPC5	ENST00000377067.9	c.1280+36581A>C		intron_variant	Intron 5 of 7	1	NM_004466.6	ENSP00000366267.3

Frequencies

GnomAD3 genomes AF: 0.360 AC: 54625 AN: 151848 Hom.: 11127 Cov.: 32

Gnomad AFR AF: 0.558

Gnomad AMI AF: 0.242

Gnomad AMR AF: 0.325

Gnomad ASJ AF: 0.343

Gnomad EAS AF: 0.246

Gnomad SAS AF: 0.180

Gnomad FIN AF: 0.325

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.277

Gnomad OTH AF: 0.352

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

GnomAD4 genome AF: 0.360 AC: 54688 AN: 151966 Hom.: 11152 Cov.: 32 AF XY: 0.355 AC XY: 26387 AN XY: 74272

African (AFR) AF: 0.558 AC: 23096 AN: 41418

American (AMR) AF: 0.325 AC: 4964 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.343 AC: 1187 AN: 3464

East Asian (EAS) AF: 0.246 AC: 1268 AN: 5158

South Asian (SAS) AF: 0.180 AC: 866 AN: 4814

European-Finnish (FIN) AF: 0.325 AC: 3432 AN: 10560

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.277 AC: 18814 AN: 67970

Other (OTH) AF: 0.354 AC: 746 AN: 2110

Alfa AF: 0.267 Hom.: 3064

Bravo AF: 0.369

Asia WGS AF: 0.267 AC: 929 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.6
DANN	Benign	0.60
PhyloP100		-0.12
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: rs2352029; hg19: chr13-92445255;