1-1615497-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The XM_047446594.1(MIB2):c.38C>A(p.Ser13Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000072 in 1,527,504 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
XM_047446594.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MIB2 | NM_001170687.4 | c.-266C>A | upstream_gene_variant | ENST00000355826.10 | NP_001164158.3 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152204Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.00000814 AC: 1AN: 122800Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 67674
GnomAD4 exome AF: 0.00000291 AC: 4AN: 1375300Hom.: 0 Cov.: 32 AF XY: 0.00000295 AC XY: 2AN XY: 678786
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152204Hom.: 0 Cov.: 34 AF XY: 0.0000538 AC XY: 4AN XY: 74374
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.38C>A (p.S13Y) alteration is located in exon 1 (coding exon 1) of the MIB2 gene. This alteration results from a C to A substitution at nucleotide position 38, causing the serine (S) at amino acid position 13 to be replaced by a tyrosine (Y). 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