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. The variant received -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
• Publications: 1 publications found

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]

GPC6 Gene-Disease associations (from GenCC):

• autosomal recessive omodysplasia

  Inheritance: AR Classification: STRONG, MODERATE, SUPPORTIVE Submitted by: Orphanet, Labcorp Genetics (formerly Invitae), Ambry Genetics, G2P

ENSG00000302670 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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
ENSG00000302670	ENST00000788637.1	n.371-15887A>G		intron_variant	Intron 2 of 2

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

African (AFR) AF: 0.0672 AC: 2789 AN: 41510

American (AMR) AF: 0.160 AC: 2436 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.134 AC: 466 AN: 3472

East Asian (EAS) AF: 0.369 AC: 1903 AN: 5160

South Asian (SAS) AF: 0.112 AC: 538 AN: 4812

European-Finnish (FIN) AF: 0.135 AC: 1428 AN: 10588

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.117 AC: 7975 AN: 68000

Other (OTH) AF: 0.120 AC: 253 AN: 2108

Alfa AF: 0.117 Hom.: 1440

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
PhyloP100		0.43
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: rs9584101; hg19: chr13-93938045;