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GeneBe

rs9301921

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_005708.5(GPC6):c.712-44993A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.156 in 152,182 control chromosomes in the GnomAD database, including 2,002 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 0.16 ( 2002 hom., cov: 32)

Consequence

GPC6
NM_005708.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.366
Variant links:
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]

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ACMG classification

Classification made for transcript

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 = 0.254 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
GPC6NM_005708.5 linkuse as main transcriptc.712-44993A>G intron_variant ENST00000377047.9
GPC6XM_017020300.2 linkuse as main transcriptc.502-44993A>G intron_variant
GPC6XM_047429990.1 linkuse as main transcriptc.502-44993A>G intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
GPC6ENST00000377047.9 linkuse as main transcriptc.712-44993A>G intron_variant 1 NM_005708.5 P1

Frequencies

GnomAD3 genomes
AF:
0.156
AC:
23742
AN:
152064
Hom.:
1999
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.120
Gnomad AMI
AF:
0.0910
Gnomad AMR
AF:
0.179
Gnomad ASJ
AF:
0.207
Gnomad EAS
AF:
0.266
Gnomad SAS
AF:
0.103
Gnomad FIN
AF:
0.183
Gnomad MID
AF:
0.139
Gnomad NFE
AF:
0.163
Gnomad OTH
AF:
0.154
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.156
AC:
23756
AN:
152182
Hom.:
2002
Cov.:
32
AF XY:
0.156
AC XY:
11641
AN XY:
74388
show subpopulations
Gnomad4 AFR
AF:
0.119
Gnomad4 AMR
AF:
0.180
Gnomad4 ASJ
AF:
0.207
Gnomad4 EAS
AF:
0.266
Gnomad4 SAS
AF:
0.102
Gnomad4 FIN
AF:
0.183
Gnomad4 NFE
AF:
0.163
Gnomad4 OTH
AF:
0.154
Alfa
AF:
0.160
Hom.:
1100
Bravo
AF:
0.159
Asia WGS
AF:
0.200
AC:
696
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
2.6
Dann
Benign
0.42

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs9301921; hg19: chr13-94634989; API