1-1623402-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_080875.5(MIB2):c.-51C>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 0.000388 in 1,599,816 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_080875.5 5_prime_UTR_premature_start_codon_gain
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MIB2 | NM_001170687.4 | c.-22-29C>T | intron_variant | Intron 2 of 19 | ENST00000355826.10 | NP_001164158.3 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000283 AC: 43AN: 152096Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000460 AC: 101AN: 219350Hom.: 1 AF XY: 0.000512 AC XY: 62AN XY: 121122
GnomAD4 exome AF: 0.000399 AC: 577AN: 1447602Hom.: 3 Cov.: 29 AF XY: 0.000456 AC XY: 328AN XY: 719706
GnomAD4 genome AF: 0.000282 AC: 43AN: 152214Hom.: 0 Cov.: 33 AF XY: 0.000322 AC XY: 24AN XY: 74428
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.295C>T (p.R99W) alteration is located in exon 3 (coding exon 3) of the MIB2 gene. This alteration results from a C to T substitution at nucleotide position 295, causing the arginine (R) at amino acid position 99 to be replaced by a tryptophan (W). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at