rs9561023

Variant names:

• chr13-92370148-G-A
• rs9561023
• NM_004466.6:c.1561+225159G>A

Your query was ambiguous. Multiple possible variants found:

• chr13-92370148-G-A
• chr13-92370148-G-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.1561+225159G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.166 in 152,164 control chromosomes in the GnomAD database, including 2,865 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 0.17 (2865 hom., cov: 33)
• Consequence: GPC5 NM_004466.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.29
• Publications: 5 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]

GPC5-AS2 (HGNC:39887): (GPC5 antisense RNA 2)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.318 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GPC5	NM_004466.6	c.1561+225159G>A		intron_variant	Intron 7 of 7	ENST00000377067.9	NP_004457.1
GPC5	XM_017020435.3	c.1561+225159G>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+225159G>A		intron_variant	Intron 7 of 7	1	NM_004466.6	ENSP00000366267.3
GPC5-AS2	ENST00000656007.1	n.165+9224C>T		intron_variant	Intron 1 of 3
GPC5-AS2	ENST00000810843.1	n.160+9224C>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.165 AC: 25133 AN: 152046 Hom.: 2845 Cov.: 33

Gnomad AFR AF: 0.322

Gnomad AMI AF: 0.0603

Gnomad AMR AF: 0.134

Gnomad ASJ AF: 0.111

Gnomad EAS AF: 0.209

Gnomad SAS AF: 0.164

Gnomad FIN AF: 0.0750

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.0923

Gnomad OTH AF: 0.156

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

GnomAD4 genome AF: 0.166 AC: 25206 AN: 152164 Hom.: 2865 Cov.: 33 AF XY: 0.166 AC XY: 12347 AN XY: 74408

African (AFR) AF: 0.323 AC: 13393 AN: 41472

American (AMR) AF: 0.134 AC: 2050 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.111 AC: 384 AN: 3468

East Asian (EAS) AF: 0.209 AC: 1082 AN: 5176

South Asian (SAS) AF: 0.164 AC: 792 AN: 4824

European-Finnish (FIN) AF: 0.0750 AC: 796 AN: 10610

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.0923 AC: 6275 AN: 68008

Other (OTH) AF: 0.157 AC: 331 AN: 2112

Alfa AF: 0.117 Hom.: 6153

Bravo AF: 0.178

Asia WGS AF: 0.198 AC: 689 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.15
DANN	Benign	0.40
PhyloP100		-1.3
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: rs9561023; hg19: chr13-93022401;