rs9584101

Variant names:

• chr13-93285792-A-G
• rs9584101
• NM_005708.5:c.160+58176A>G

Your query was ambiguous. Multiple possible variants found:

• chr13-93285792-A-G
• chr13-93285792-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_005708.5(GPC6):​c.160+58176A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.119 in 152,114 control chromosomes in the GnomAD database, including 1,334 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 0.12 (1334 hom., cov: 31)
• Consequence: GPC6 NM_005708.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.433

Genes affected

GPC6 (HGNC:4454): (glypican 6) The glypicans comprise a family of glycosylphosphatidylinositol-anchored heparan sulfate proteoglycans, and they have been implicated in the control of cell growth and cell division. The glypican encoded by this gene is a putative cell surface coreceptor for growth factors, extracellular matrix proteins, proteases and anti-proteases. Mutations in this gene are associated with omodysplasia 1. [provided by RefSeq, Nov 2016]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.355 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GPC6	NM_005708.5	c.160+58176A>G		intron_variant	Intron 1 of 8	ENST00000377047.9	NP_005699.1
GPC6	XM_047429990.1	c.-51+59110A>G		intron_variant	Intron 1 of 8		XP_047285946.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GPC6	ENST00000377047.9	c.160+58176A>G		intron_variant	Intron 1 of 8	1	NM_005708.5	ENSP00000366246.3

Frequencies

GnomAD3 genomes AF: 0.119 AC: 18033 AN: 151994 Hom.: 1333 Cov.: 31

Gnomad AFR AF: 0.0674

Gnomad AMI AF: 0.237

Gnomad AMR AF: 0.159

Gnomad ASJ AF: 0.134

Gnomad EAS AF: 0.368

Gnomad SAS AF: 0.111

Gnomad FIN AF: 0.135

Gnomad MID AF: 0.124

Gnomad NFE AF: 0.117

Gnomad OTH AF: 0.119

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

GnomAD4 genome AF: 0.119 AC: 18042 AN: 152114 Hom.: 1334 Cov.: 31 AF XY: 0.121 AC XY: 8999 AN XY: 74362

Gnomad4 AFR AF: 0.0672

Gnomad4 AMR AF: 0.160

Gnomad4 ASJ AF: 0.134

Gnomad4 EAS AF: 0.369

Gnomad4 SAS AF: 0.112

Gnomad4 FIN AF: 0.135

Gnomad4 NFE AF: 0.117

Gnomad4 OTH AF: 0.120

Alfa AF: 0.110 Hom.: 941

Bravo AF: 0.125

Asia WGS AF: 0.203 AC: 704 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	7.3
DANN	Benign	0.87

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

Publications

LitVar

Other links and lift over

dbSNP: rs9584101; hg19: chr13-93938045;