4-6293966-C-G
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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
NM_006005.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.04
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]
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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 |
---|---|---|---|---|---|---|---|---|
WFS1 | NM_006005.3 | c.713-1075C>G | intron_variant | ENST00000226760.5 | NP_005996.2 | |||
WFS1 | NM_001145853.1 | c.713-1075C>G | intron_variant | NP_001139325.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.632 AC: 96092AN: 151954Hom.: 30991 Cov.: 33
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.632 AC: 96182AN: 152072Hom.: 31031 Cov.: 33 AF XY: 0.635 AC XY: 47204AN XY: 74320
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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 submitter | clinical testing | GeneDx | Jun 14, 2018 | This 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 submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Wolfram syndrome 1 Benign:2
Benign, criteria provided, single submitter | research | Clinical 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 submitter | clinical testing | Mendelics | May 28, 2019 | - - |
Type 2 diabetes mellitus Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Mar 06, 2024 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | research | H3Africa Consortium | Oct 28, 2020 | While 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 provided | curation | Reproductive Health Research and Development, BGI Genomics | Jan 06, 2020 | NG_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
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at