4-6269920-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_006005.3(WFS1):c.-100C>T variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000657 in 152,224 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_006005.3 5_prime_UTR_premature_start_codon_gain
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
WFS1 | NM_006005.3 | c.-100C>T | 5_prime_UTR_premature_start_codon_gain_variant | Exon 1 of 8 | ENST00000226760.5 | NP_005996.2 | ||
WFS1 | NM_006005.3 | c.-100C>T | 5_prime_UTR_variant | Exon 1 of 8 | ENST00000226760.5 | NP_005996.2 | ||
WFS1 | NM_001145853.1 | c.-96C>T | 5_prime_UTR_premature_start_codon_gain_variant | Exon 1 of 8 | NP_001139325.1 | |||
WFS1 | NM_001145853.1 | c.-96C>T | 5_prime_UTR_variant | Exon 1 of 8 | NP_001139325.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
WFS1 | ENST00000226760 | c.-100C>T | 5_prime_UTR_premature_start_codon_gain_variant | Exon 1 of 8 | 1 | NM_006005.3 | ENSP00000226760.1 | |||
WFS1 | ENST00000226760 | c.-100C>T | 5_prime_UTR_variant | Exon 1 of 8 | 1 | NM_006005.3 | ENSP00000226760.1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152224Hom.: 0 Cov.: 34
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 10Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 8
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152224Hom.: 0 Cov.: 34 AF XY: 0.00 AC XY: 0AN XY: 74364
ClinVar
Submissions by phenotype
Wolfram syndrome 1 Benign:1
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 rs886059524 yet. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at