chr1-1615512-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001170687.4(MIB2):c.-251C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000508 in 1,377,712 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 Uncertain significance (★).
Frequency
Consequence
NM_001170687.4 5_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MIB2 | NM_001170687.4 | c.-251C>T | 5_prime_UTR_variant | Exon 1 of 20 | ENST00000355826.10 | NP_001164158.3 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 34
GnomAD3 exomes AF: 0.0000238 AC: 3AN: 126110Hom.: 0 AF XY: 0.0000434 AC XY: 3AN XY: 69152
GnomAD4 exome AF: 0.00000508 AC: 7AN: 1377712Hom.: 0 Cov.: 32 AF XY: 0.00000588 AC XY: 4AN XY: 680012
GnomAD4 genome Cov.: 34
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.53C>T (p.P18L) alteration is located in exon 1 (coding exon 1) of the MIB2 gene. This alteration results from a C to T substitution at nucleotide position 53, causing the proline (P) at amino acid position 18 to be replaced by a leucine (L). 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