10-110207875-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_130439.3(MXI1):c.67C>A(p.Pro23Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000041 in 1,242,394 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 11/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_130439.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MXI1 | ENST00000332674.9 | c.67C>A | p.Pro23Thr | missense_variant | Exon 1 of 6 | 1 | NM_130439.3 | ENSP00000331152.5 | ||
MXI1 | ENST00000453116.5 | c.67C>A | p.Pro23Thr | missense_variant | Exon 1 of 4 | 5 | ENSP00000398981.1 | |||
ENSG00000228417 | ENST00000451656.1 | n.445G>T | non_coding_transcript_exon_variant | Exon 3 of 3 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000535 AC: 8AN: 149436Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000370 AC: 1AN: 27020Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 16322
GnomAD4 exome AF: 0.0000393 AC: 43AN: 1092848Hom.: 0 Cov.: 29 AF XY: 0.0000434 AC XY: 23AN XY: 529354
GnomAD4 genome AF: 0.0000535 AC: 8AN: 149546Hom.: 0 Cov.: 31 AF XY: 0.0000411 AC XY: 3AN XY: 73002
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.67C>A (p.P23T) alteration is located in exon 1 (coding exon 1) of the MXI1 gene. This alteration results from a C to A substitution at nucleotide position 67, causing the proline (P) at amino acid position 23 to be replaced by a threonine (T). 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