13-93829971-A-G

Position:

• chr13-93829971-A-G

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_005708.5(GPC6):​c.320-183A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0399 in 152,274 control chromosomes in the GnomAD database, including 294 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.040 (294 hom., cov: 31)
• Consequence: GPC6 NM_005708.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.0570

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-AS2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BP6: Variant 13-93829971-A-G is Benign according to our data. Variant chr13-93829971-A-G is described in ClinVar as [Benign]. Clinvar id is 1275224.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.113 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GPC6	NM_005708.5	c.320-183A>G		intron_variant		ENST00000377047.9	NP_005699.1
GPC6	XM_017020300.2	c.110-183A>G		intron_variant			XP_016875789.1
GPC6	XM_047429990.1	c.110-183A>G		intron_variant			XP_047285946.1
GPC6-AS2	NR_046536.1	n.380+845T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GPC6	ENST00000377047.9	c.320-183A>G		intron_variant		1	NM_005708.5	ENSP00000366246.3
GPC6-AS2	ENST00000445540.1	n.228+845T>C		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.0399 AC: 6072 AN: 152156 Hom.: 291 Cov.: 31

Gnomad AFR AF: 0.116

Gnomad AMI AF: 0.00548

Gnomad AMR AF: 0.0221

Gnomad ASJ AF: 0.0121

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0124

Gnomad FIN AF: 0.0127

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.00847

Gnomad OTH AF: 0.0382

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

GnomAD4 genome AF: 0.0399 AC: 6083 AN: 152274 Hom.: 294 Cov.: 31 AF XY: 0.0386 AC XY: 2873 AN XY: 74456

Gnomad4 AFR AF: 0.116

Gnomad4 AMR AF: 0.0220

Gnomad4 ASJ AF: 0.0121

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0122

Gnomad4 FIN AF: 0.0127

Gnomad4 NFE AF: 0.00847

Gnomad4 OTH AF: 0.0383

Alfa AF: 0.0206 Hom.: 39

Bravo AF: 0.0442

Asia WGS AF: 0.0110 AC: 39 AN: 3476

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 16, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.9
DANN	Benign	0.53

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

Other links and lift over

dbSNP: rs7139626; hg19: chr13-94482224;