Variant 15-51342058-T-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_181789.4(GLDN):c.363+11T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.476 in 1,589,880 control chromosomes in the GnomAD database, including 188,404 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.57 ( 26945 hom., cov: 34)

Exomes 𝑓: 0.47 ( 161459 hom. )

Consequence

GLDN
NM_181789.4 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.443

Variant links:

Genes affected

GLDN (HGNC:29514): (gliomedin) This gene encodes a protein that contains olfactomedin-like and collagen-like domains. The encoded protein, which exists in both transmembrane and secreted forms, promotes formation of the nodes of Ranvier in the peripheral nervous system. Mutations in this gene cause a form of lethal congenital contracture syndrome in human patients. Autoantibodies to the encoded protein have been identified in sera form patients with multifocal motor neuropathy. [provided by RefSeq, May 2017]

GLDN links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.55).

BP6

Variant 15-51342058-T-G is Benign according to our data. Variant chr15-51342058-T-G is described in ClinVar as [Benign]. Clinvar id is 1262424.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.837 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GLDN	NM_181789.4 linkuse as main transcript	c.363+11T>G		intron_variant		ENST00000335449.11

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GLDN	ENST00000335449.11 linkuse as main transcript	c.363+11T>G	intron_variant		2	NM_181789.4	P1	Q6ZMI3-1
GLDN	ENST00000560690.5 linkuse as main transcript	n.113T>G	non_coding_transcript_exon_variant	1/4	1
GLDN	ENST00000558286.5 linkuse as main transcript	n.174+11T>G	intron_variant, non_coding_transcript_variant		1
GLDN	ENST00000560215.5 linkuse as main transcript	c.250+11T>G	intron_variant		4

Frequencies

GnomAD3 genomes

AF:

0.565

AC:

85793

AN:

151892

Hom.:

26872

Cov.:

show subpopulations

Gnomad AFR

AF:

0.844

Gnomad AMI

AF:

0.386

Gnomad AMR

AF:

0.578

Gnomad ASJ

AF:

0.435

Gnomad EAS

AF:

0.585

Gnomad SAS

AF:

0.514

Gnomad FIN

AF:

0.306

Gnomad MID

AF:

0.364

Gnomad NFE

AF:

0.444

Gnomad OTH

AF:

0.551

GnomAD3 exomes

AF:

0.503

AC:

109764

AN:

218298

Hom.:

29215

AF XY:

0.490

AC XY:

59158

AN XY:

120656

show subpopulations

Gnomad AFR exome

AF:

0.851

Gnomad AMR exome

AF:

0.613

Gnomad ASJ exome

AF:

0.424

Gnomad EAS exome

AF:

0.580

Gnomad SAS exome

AF:

0.493

Gnomad FIN exome

AF:

0.325

Gnomad NFE exome

AF:

0.441

Gnomad OTH exome

AF:

0.479

GnomAD4 exome

AF:

0.466

AC:

670664

AN:

1437870

Hom.:

161459

Cov.:

AF XY:

0.465

AC XY:

332468

AN XY:

715700

show subpopulations

Gnomad4 AFR exome

AF:

0.864

Gnomad4 AMR exome

AF:

0.612

Gnomad4 ASJ exome

AF:

0.427

Gnomad4 EAS exome

AF:

0.599

Gnomad4 SAS exome

AF:

0.483

Gnomad4 FIN exome

AF:

0.334

Gnomad4 NFE exome

AF:

0.448

Gnomad4 OTH exome

AF:

0.490

GnomAD4 genome

AF:

0.565

AC:

85926

AN:

152010

Hom.:

26945

Cov.:

AF XY:

0.559

AC XY:

41499

AN XY:

74294

show subpopulations

Gnomad4 AFR

AF:

0.844

Gnomad4 AMR

AF:

0.578

Gnomad4 ASJ

AF:

0.435

Gnomad4 EAS

AF:

0.586

Gnomad4 SAS

AF:

0.513

Gnomad4 FIN

AF:

0.306

Gnomad4 NFE

AF:

0.444

Gnomad4 OTH

AF:

0.554

Alfa

AF:

0.482

Hom.:

3523

Bravo

AF:

0.602

Asia WGS

AF:

0.582

AC:

2021

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Aug 02, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.55

CADD

Benign

DANN

Benign

0.69

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over