rs11839514

Variant summary

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

The NM_005708.5(GPC6):​c.160+58837A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.374 in 151,986 control chromosomes in the GnomAD database, including 10,736 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 0.37 ( 10736 hom., cov: 32)

Consequence

GPC6
NM_005708.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0140
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=-0.74).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.438 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
GPC6NM_005708.5 linkuse as main transcriptc.160+58837A>G intron_variant ENST00000377047.9
GPC6XM_047429990.1 linkuse as main transcriptc.-51+59771A>G intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
GPC6ENST00000377047.9 linkuse as main transcriptc.160+58837A>G intron_variant 1 NM_005708.5 P1

Frequencies

GnomAD3 genomes
AF:
0.373
AC:
56691
AN:
151868
Hom.:
10709
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.416
Gnomad AMI
AF:
0.325
Gnomad AMR
AF:
0.394
Gnomad ASJ
AF:
0.276
Gnomad EAS
AF:
0.453
Gnomad SAS
AF:
0.292
Gnomad FIN
AF:
0.371
Gnomad MID
AF:
0.323
Gnomad NFE
AF:
0.349
Gnomad OTH
AF:
0.349
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.374
AC:
56779
AN:
151986
Hom.:
10736
Cov.:
32
AF XY:
0.374
AC XY:
27757
AN XY:
74296
show subpopulations
Gnomad4 AFR
AF:
0.417
Gnomad4 AMR
AF:
0.395
Gnomad4 ASJ
AF:
0.276
Gnomad4 EAS
AF:
0.453
Gnomad4 SAS
AF:
0.292
Gnomad4 FIN
AF:
0.371
Gnomad4 NFE
AF:
0.349
Gnomad4 OTH
AF:
0.357
Alfa
AF:
0.355
Hom.:
8389
Bravo
AF:
0.384
Asia WGS
AF:
0.394
AC:
1370
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.74
CADD
Benign
9.4
DANN
Benign
0.90

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: rs11839514; hg19: chr13-93938706; API