NM_001170687.4:c.-8C>T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_001170687.4(MIB2):c.-8C>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 0.0000225 in 1,600,800 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001170687.4 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
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MIB2 | ENST00000355826 | c.-8C>T | 5_prime_UTR_premature_start_codon_gain_variant | Exon 3 of 20 | 1 | NM_001170687.4 | ENSP00000348081.6 | |||
MIB2 | ENST00000355826 | c.-8C>T | 5_prime_UTR_variant | Exon 3 of 20 | 1 | NM_001170687.4 | ENSP00000348081.6 |
Frequencies
GnomAD3 genomes AF: 0.0000591 AC: 9AN: 152194Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.0000323 AC: 7AN: 216842Hom.: 0 AF XY: 0.0000335 AC XY: 4AN XY: 119546
GnomAD4 exome AF: 0.0000186 AC: 27AN: 1448606Hom.: 1 Cov.: 34 AF XY: 0.0000181 AC XY: 13AN XY: 720000
GnomAD4 genome AF: 0.0000591 AC: 9AN: 152194Hom.: 0 Cov.: 34 AF XY: 0.0000403 AC XY: 3AN XY: 74352
ClinVar
Submissions by phenotype
not specified Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at