4-6293966-C-G

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_006005.3(WFS1):​c.713-1075C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.632 in 152,072 control chromosomes in the GnomAD database, including 31,031 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.63 ( 31031 hom., cov: 33)

Consequence

WFS1
NM_006005.3 intron

Scores

2

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts P:1B:6

Conservation

PhyloP100: 1.04
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 -20 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BP6
Variant 4-6293966-C-G is Benign according to our data. Variant chr4-6293966-C-G is described in ClinVar as [Benign]. Clinvar id is 4528.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.91 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
WFS1NM_006005.3 linkc.713-1075C>G intron_variant ENST00000226760.5 NP_005996.2 O76024A0A0S2Z4V6
WFS1NM_001145853.1 linkc.713-1075C>G intron_variant NP_001139325.1 O76024A0A0S2Z4V6

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
WFS1ENST00000226760.5 linkc.713-1075C>G intron_variant 1 NM_006005.3 ENSP00000226760.1 O76024

Frequencies

GnomAD3 genomes
AF:
0.632
AC:
96092
AN:
151954
Hom.:
30991
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.645
Gnomad AMI
AF:
0.384
Gnomad AMR
AF:
0.693
Gnomad ASJ
AF:
0.671
Gnomad EAS
AF:
0.932
Gnomad SAS
AF:
0.703
Gnomad FIN
AF:
0.566
Gnomad MID
AF:
0.652
Gnomad NFE
AF:
0.594
Gnomad OTH
AF:
0.650
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.632
AC:
96182
AN:
152072
Hom.:
31031
Cov.:
33
AF XY:
0.635
AC XY:
47204
AN XY:
74320
show subpopulations
Gnomad4 AFR
AF:
0.645
Gnomad4 AMR
AF:
0.694
Gnomad4 ASJ
AF:
0.671
Gnomad4 EAS
AF:
0.932
Gnomad4 SAS
AF:
0.702
Gnomad4 FIN
AF:
0.566
Gnomad4 NFE
AF:
0.594
Gnomad4 OTH
AF:
0.653
Alfa
AF:
0.612
Hom.:
3548
Bravo
AF:
0.642
Asia WGS
AF:
0.812
AC:
2824
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Pathogenic:1Benign:6
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not provided Benign:2
Benign, criteria provided, single submitterclinical testingGeneDxJun 14, 2018This 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 submitternot providedBreakthrough Genomics, Breakthrough Genomics-- -
Wolfram syndrome 1 Benign:2
Benign, criteria provided, single submitterresearchClinical Genomics, Uppaluri K&H Personalized Medicine Clinic-Mutations in WFS1 gene are associated with Wolfram's syndrome, an autosomal recessive condition, which cause diabetes mellitus, diabetes insipidus, deafness and optic atrophy. rs6446482 variant is also seen in patients with Diabetes Mellitus. However, the role of this particular variant is yet to be ascertained. -
Benign, criteria provided, single submitterclinical testingMendelicsMay 28, 2019- -
Type 2 diabetes mellitus Pathogenic:1
Pathogenic, no assertion criteria providedliterature onlyOMIMMar 06, 2024- -
not specified Benign:1
Benign, criteria provided, single submitterresearchH3Africa ConsortiumOct 28, 2020While the frequency of the alternate allele in gnoMAD v2.0.2 is 0.707, its frequency in African populations is >5%. This suggests that previous classifications of this variant as pathogenic are in error. -
Diabetes mellitus, noninsulin-dependent, association with Benign:1
Benign, no assertion criteria providedcurationReproductive Health Research and Development, BGI GenomicsJan 06, 2020NG_011700.1(NM_006005.3):c.713-1075C>G (rs6446482) in the WFS1 gene has an allele frequency of 0.647 in African subpopulation in the gnomAD database, including 6277 homozygous. This evidence suggests the variant to be classified as benign. ACMG/AMP criteria applied: BA1, BS2. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
5.9
DANN
Benign
0.70

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: rs6446482; hg19: chr4-6295693; API