13-94357008-G-A
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_005708.5(GPC6):c.1153-25406G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.221 in 152,108 control chromosomes in the GnomAD database, including 4,183 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 0.22 ( 4183 hom., cov: 32)
Consequence
GPC6
NM_005708.5 intron
NM_005708.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.426
Publications
0 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 omodysplasiaInheritance: AR Classification: STRONG, MODERATE, SUPPORTIVE Submitted by: Orphanet, Labcorp Genetics (formerly Invitae), Ambry Genetics, G2P
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.99).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.297 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GPC6 | NM_005708.5 | c.1153-25406G>A | intron_variant | Intron 6 of 8 | ENST00000377047.9 | NP_005699.1 | ||
GPC6 | XM_017020300.2 | c.943-25406G>A | intron_variant | Intron 6 of 8 | XP_016875789.1 | |||
GPC6 | XM_047429990.1 | c.943-25406G>A | intron_variant | Intron 6 of 8 | XP_047285946.1 | |||
GPC6 | XM_017020302.2 | c.460-25406G>A | intron_variant | Intron 3 of 5 | XP_016875791.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.221 AC: 33578AN: 151988Hom.: 4179 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
33578
AN:
151988
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.221 AC: 33606AN: 152108Hom.: 4183 Cov.: 32 AF XY: 0.217 AC XY: 16113AN XY: 74342 show subpopulations
GnomAD4 genome
AF:
AC:
33606
AN:
152108
Hom.:
Cov.:
32
AF XY:
AC XY:
16113
AN XY:
74342
show subpopulations
African (AFR)
AF:
AC:
6156
AN:
41500
American (AMR)
AF:
AC:
4648
AN:
15286
Ashkenazi Jewish (ASJ)
AF:
AC:
999
AN:
3468
East Asian (EAS)
AF:
AC:
19
AN:
5172
South Asian (SAS)
AF:
AC:
528
AN:
4810
European-Finnish (FIN)
AF:
AC:
2077
AN:
10584
Middle Eastern (MID)
AF:
AC:
103
AN:
294
European-Non Finnish (NFE)
AF:
AC:
18311
AN:
67972
Other (OTH)
AF:
AC:
571
AN:
2110
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
1325
2651
3976
5302
6627
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
348
696
1044
1392
1740
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
293
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.