rs7175922

Positions:

• chr15-51354540-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_181789.4(GLDN):​c.363+12493G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.239 in 152,094 control chromosomes in the GnomAD database, including 6,662 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 0.24 (6662 hom., cov: 32)
• Consequence: GLDN NM_181789.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.299

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.509 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GLDN	NM_181789.4	c.363+12493G>A		intron_variant		ENST00000335449.11	NP_861454.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GLDN	ENST00000335449.11	c.363+12493G>A		intron_variant		2	NM_181789.4	ENSP00000335196.6
GLDN	ENST00000558286.5	n.174+12493G>A		intron_variant		1
GLDN	ENST00000560690.5	n.140+12455G>A		intron_variant		1
GLDN	ENST00000560215.5	c.249+12493G>A		intron_variant		4		ENSP00000484633.1

Frequencies

GnomAD3 genomes AF: 0.238 AC: 36191 AN: 151976 Hom.: 6636 Cov.: 32

Gnomad AFR AF: 0.514

Gnomad AMI AF: 0.110

Gnomad AMR AF: 0.182

Gnomad ASJ AF: 0.141

Gnomad EAS AF: 0.207

Gnomad SAS AF: 0.275

Gnomad FIN AF: 0.0631

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.118

Gnomad OTH AF: 0.218

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

GnomAD4 genome AF: 0.239 AC: 36278 AN: 152094 Hom.: 6662 Cov.: 32 AF XY: 0.237 AC XY: 17608 AN XY: 74386

Gnomad4 AFR AF: 0.514

Gnomad4 AMR AF: 0.183

Gnomad4 ASJ AF: 0.141

Gnomad4 EAS AF: 0.207

Gnomad4 SAS AF: 0.274

Gnomad4 FIN AF: 0.0631

Gnomad4 NFE AF: 0.118

Gnomad4 OTH AF: 0.221

Alfa AF: 0.177 Hom.: 485

Bravo AF: 0.258

Asia WGS AF: 0.297 AC: 1033 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	5.6
DANN	Benign	0.71

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: rs7175922; hg19: chr15-51646737;