Variant 13-93347691-C-T details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_005708.5(GPC6):c.160+120075C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.118 in 152,146 control chromosomes in the GnomAD database, including 1,409 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 ( 1409 hom., cov: 32)

Consequence

GPC6
NM_005708.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.43

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]

GPC6 links:

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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 = 0.352 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GPC6	NM_005708.5 link	c.160+120075C>T		intron_variant		ENST00000377047.9	NP_005699.1	Q9Y625
GPC6	XM_047429990.1 link	c.-51+121009C>T		intron_variant			XP_047285946.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GPC6	ENST00000377047.9 link	c.160+120075C>T		intron_variant		1	NM_005708.5	ENSP00000366246.3		Q9Y625

Frequencies

GnomAD3 genomes

AF:

0.118

AC:

17959

AN:

152028

Hom.:

1407

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0837

Gnomad AMI

AF:

0.0351

Gnomad AMR

AF:

0.213

Gnomad ASJ

AF:

0.122

Gnomad EAS

AF:

0.364

Gnomad SAS

AF:

0.116

Gnomad FIN

AF:

0.157

Gnomad MID

AF:

0.136

Gnomad NFE

AF:

0.0937

Gnomad OTH

AF:

0.127

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

GnomAD4 genome

AF:

0.118

AC:

17972

AN:

152146

Hom.:

1409

Cov.:

AF XY:

0.125

AC XY:

9261

AN XY:

74382

show subpopulations

Gnomad4 AFR

AF:

0.0837

Gnomad4 AMR

AF:

0.213

Gnomad4 ASJ

AF:

0.122

Gnomad4 EAS

AF:

0.366

Gnomad4 SAS

AF:

0.116

Gnomad4 FIN

AF:

0.157

Gnomad4 NFE

AF:

0.0937

Gnomad4 OTH

AF:

0.125

Alfa

AF:

0.0469

Hom.:

Bravo

AF:

0.125

Asia WGS

AF:

0.211

AC:

734

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

0.50

DANN

Benign

0.61

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over