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15-51341864-C-T

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_ModerateBP6_ModerateBP7BA1

The NM_181789.4(GLDN):c.180C>T(p.Arg60=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00889 in 1,548,716 control chromosomes in the GnomAD database, including 1,041 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.047 ( 560 hom., cov: 33)
Exomes 𝑓: 0.0047 ( 481 hom. )

Consequence

GLDN
NM_181789.4 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.567
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.38).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 15-51341864-C-T is Benign according to our data. Variant chr15-51341864-C-T is described in ClinVar as [Benign]. Clinvar id is 1272774.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=-0.567 with no splicing effect.
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.16 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
GLDNNM_181789.4 linkuse as main transcriptc.180C>T p.Arg60= synonymous_variant 1/10 ENST00000335449.11
GLDNXM_017022121.2 linkuse as main transcriptc.180C>T p.Arg60= synonymous_variant 1/9
GLDNXM_017022125.1 linkuse as main transcriptc.180C>T p.Arg60= synonymous_variant 1/10

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
GLDNENST00000335449.11 linkuse as main transcriptc.180C>T p.Arg60= synonymous_variant 1/102 NM_181789.4 P1Q6ZMI3-1
GLDNENST00000560215.5 linkuse as main transcriptc.69C>T p.Arg23= synonymous_variant 1/44
GLDNENST00000558286.5 linkuse as main transcript upstream_gene_variant 1

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0469
AC:
7136
AN:
152128
Hom.:
559
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.164
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0168
Gnomad ASJ
AF:
0.000288
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000414
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00955
Gnomad NFE
AF:
0.000456
Gnomad OTH
AF:
0.0310
GnomAD3 exomes
AF:
0.00963
AC:
1446
AN:
150148
Hom.:
117
AF XY:
0.00765
AC XY:
640
AN XY:
83624
show subpopulations
Gnomad AFR exome
AF:
0.183
Gnomad AMR exome
AF:
0.00760
Gnomad ASJ exome
AF:
0.000976
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.000280
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000437
Gnomad OTH exome
AF:
0.00535
GnomAD4 exome
AF:
0.00475
AC:
6629
AN:
1396476
Hom.:
481
Cov.:
30
AF XY:
0.00411
AC XY:
2841
AN XY:
691158
show subpopulations
Gnomad4 AFR exome
AF:
0.171
Gnomad4 AMR exome
AF:
0.00900
Gnomad4 ASJ exome
AF:
0.000755
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.000380
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.000301
Gnomad4 OTH exome
AF:
0.0106
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0469
AC:
7144
AN:
152240
Hom.:
560
Cov.:
33
AF XY:
0.0455
AC XY:
3387
AN XY:
74450
show subpopulations
Gnomad4 AFR
AF:
0.163
Gnomad4 AMR
AF:
0.0167
Gnomad4 ASJ
AF:
0.000288
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000207
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000456
Gnomad4 OTH
AF:
0.0307
Alfa
AF:
0.0251
Hom.:
48
Bravo
AF:
0.0527
Asia WGS
AF:
0.00637
AC:
22
AN:
3466

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 submitterclinical testingGeneDxMay 04, 2021- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.38
Cadd
Benign
12
Dann
Benign
0.93

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: rs139283412; hg19: chr15-51634061; API