rs146114074

Positions:

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2

The NM_006005.3(WFS1):ā€‹c.917T>Cā€‹(p.Met306Thr) variant causes a missense change. The variant allele was found at a frequency of 0.000683 in 1,614,058 control chromosomes in the GnomAD database, including 9 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

Frequency

Genomes: š‘“ 0.0036 ( 3 hom., cov: 32)
Exomes š‘“: 0.00038 ( 6 hom. )

Consequence

WFS1
NM_006005.3 missense

Scores

2
16

Clinical Significance

Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:1B:11

Conservation

PhyloP100: 3.75
Variant links:
Genes affected
WFS1 (HGNC:12762): (wolframin ER transmembrane glycoprotein) This gene encodes a transmembrane protein, which is located primarily in the endoplasmic reticulum and ubiquitously expressed with highest levels in brain, pancreas, heart, and insulinoma beta-cell lines. Mutations in this gene are associated with Wolfram syndrome, also called DIDMOAD (Diabetes Insipidus, Diabetes Mellitus, Optic Atrophy, and Deafness), an autosomal recessive disorder. The disease affects the brain and central nervous system. Mutations in this gene can also cause autosomal dominant deafness 6 (DFNA6), also known as DFNA14 or DFNA38. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Mar 2009]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=0.0090482235).
BP6
Variant 4-6300712-T-C is Benign according to our data. Variant chr4-6300712-T-C is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 167850.We mark this variant Likely_benign, oryginal submissions are: {Uncertain_significance=1, Benign=9}. Variant chr4-6300712-T-C is described in Lovd as [Benign].
BS2
High Homozygotes in GnomAd4 at 3 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
WFS1NM_006005.3 linkuse as main transcriptc.917T>C p.Met306Thr missense_variant 8/8 ENST00000226760.5 NP_005996.2 O76024A0A0S2Z4V6
WFS1NM_001145853.1 linkuse as main transcriptc.917T>C p.Met306Thr missense_variant 8/8 NP_001139325.1 O76024A0A0S2Z4V6

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
WFS1ENST00000226760.5 linkuse as main transcriptc.917T>C p.Met306Thr missense_variant 8/81 NM_006005.3 ENSP00000226760.1 O76024

Frequencies

GnomAD3 genomes
AF:
0.00360
AC:
548
AN:
152086
Hom.:
3
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0129
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000458
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000207
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000294
Gnomad OTH
AF:
0.00144
GnomAD3 exomes
AF:
0.000982
AC:
247
AN:
251440
Hom.:
2
AF XY:
0.000787
AC XY:
107
AN XY:
135900
show subpopulations
Gnomad AFR exome
AF:
0.0137
Gnomad AMR exome
AF:
0.000550
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.0000327
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000264
Gnomad OTH exome
AF:
0.000163
GnomAD4 exome
AF:
0.000379
AC:
554
AN:
1461854
Hom.:
6
Cov.:
31
AF XY:
0.000309
AC XY:
225
AN XY:
727234
show subpopulations
Gnomad4 AFR exome
AF:
0.0138
Gnomad4 AMR exome
AF:
0.000559
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000348
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000207
Gnomad4 OTH exome
AF:
0.000662
GnomAD4 genome
AF:
0.00360
AC:
548
AN:
152204
Hom.:
3
Cov.:
32
AF XY:
0.00341
AC XY:
254
AN XY:
74416
show subpopulations
Gnomad4 AFR
AF:
0.0129
Gnomad4 AMR
AF:
0.000458
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000207
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000294
Gnomad4 OTH
AF:
0.00142
Alfa
AF:
0.000752
Hom.:
1
Bravo
AF:
0.00418
ESP6500AA
AF:
0.0120
AC:
53
ESP6500EA
AF:
0.00
AC:
0
ExAC
AF:
0.00120
AC:
146

ClinVar

Significance: Conflicting classifications of pathogenicity
Submissions summary: Uncertain:1Benign:11
Revision: criteria provided, conflicting classifications
LINK: link

Submissions by phenotype

not specified Benign:4
Benign, criteria provided, single submitterclinical testingLaboratory for Molecular Medicine, Mass General Brigham Personalized MedicineApr 30, 2012Met306Thr in Exon 08 of WFS1: This variant is not expected to have clinical sign ificance because it has been identified in 1.2% (45/3738) of African American ch romosomes from a broad population by the NHLBI Exome Sequencing Project (http:// evs.gs.washington.edu/EVS; dbSNP rs146114074). -
Benign, criteria provided, single submitterclinical testingGeneDxJun 10, 2015This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
Benign, criteria provided, single submitterclinical testingEurofins Ntd Llc (ga)Jan 31, 2014- -
Benign, no assertion criteria providedclinical testingClinical Genetics, Academic Medical Center-- -
not provided Benign:4
Benign, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpJan 22, 2024- -
Likely benign, no assertion criteria providedclinical testingLaboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC)-- -
Benign, criteria provided, single submitterclinical testingARUP Laboratories, Molecular Genetics and Genomics, ARUP LaboratoriesSep 15, 2023- -
Benign, criteria provided, single submitternot providedBreakthrough Genomics, Breakthrough Genomics-- -
Wolfram syndrome 1 Uncertain:1
Uncertain significance, criteria provided, single submitterresearchClinical Genomics, Uppaluri K&H Personalized Medicine Clinic-Potent mutations in WFS1 gene are associated with Wolfram's syndrome, an autosomal recessive condition, which cause diabetes mellitus, diabetes insipidus, deafness and optic atrophy.However no sufficient evidence is found to ascertain the role of this particular variant rs146114074 yet. -
WFS1-Related Spectrum Disorders Benign:1
Benign, criteria provided, single submitterclinical testingIllumina Laboratory Services, IlluminaJan 13, 2018This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
Monogenic diabetes Benign:1
Benign, criteria provided, single submitterresearchPersonalized Diabetes Medicine Program, University of Maryland School of MedicineMay 18, 2018ACMG criteria: BP4 (8 predictors, Revel score 0.141; 2 predictors for PP3, not using), BS1 (1.4% in 1000G African, 1.3% in gnomAD African), BS2 (37 cases and 31 controls in type2diabetesgenetics.org; 3 homozygotes in gnomAD African)= benign -
Autosomal dominant nonsyndromic hearing loss 6 Benign:1
Benign, criteria provided, single submitterclinical testingIllumina Laboratory Services, IlluminaJan 13, 2018This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.14
BayesDel_addAF
Benign
-0.33
T
BayesDel_noAF
Benign
-0.23
CADD
Benign
17
DANN
Benign
0.74
DEOGEN2
Benign
0.064
T;T
Eigen
Benign
-0.018
Eigen_PC
Benign
0.10
FATHMM_MKL
Uncertain
0.94
D
LIST_S2
Uncertain
0.87
.;D
MetaRNN
Benign
0.0090
T;T
MetaSVM
Benign
-1.1
T
MutationAssessor
Benign
0.0
N;N
PrimateAI
Benign
0.34
T
PROVEAN
Benign
-0.42
N;N
REVEL
Benign
0.26
Sift
Benign
0.86
T;T
Sift4G
Benign
0.16
T;T
Polyphen
0.0010
B;B
Vest4
0.16
MVP
0.95
ClinPred
0.0027
T
GERP RS
4.6
Varity_R
0.041
gMVP
0.67

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: rs146114074; hg19: chr4-6302439; COSMIC: COSV99073308; API