chr7-157005558-G-C
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_005515.4(MNX1):āc.1168C>Gā(p.Pro390Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000077 in 1,558,368 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_005515.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MNX1 | NM_005515.4 | c.1168C>G | p.Pro390Ala | missense_variant | 3/3 | ENST00000252971.11 | |
MNX1 | NM_001165255.2 | c.532C>G | p.Pro178Ala | missense_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MNX1 | ENST00000252971.11 | c.1168C>G | p.Pro390Ala | missense_variant | 3/3 | 1 | NM_005515.4 | P2 | |
MNX1 | ENST00000543409.5 | c.532C>G | p.Pro178Ala | missense_variant | 3/3 | 1 | A2 | ||
MNX1 | ENST00000469500.5 | c.55+3440C>G | intron_variant | 1 | |||||
MNX1 | ENST00000479817.1 | c.38+4102C>G | intron_variant | 1 |
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 151986Hom.: 0 Cov.: 33
GnomAD4 exome AF: 0.00000782 AC: 11AN: 1406382Hom.: 0 Cov.: 31 AF XY: 0.00000861 AC XY: 6AN XY: 696804
GnomAD4 genome AF: 0.00000658 AC: 1AN: 151986Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74230
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Sep 15, 2022 | In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Tolerated"; PolyPhen-2: "Not Available"; Align-GVGD: "Class C0"). This variant has not been reported in the literature in individuals affected with MNX1-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces proline, which is neutral and non-polar, with alanine, which is neutral and non-polar, at codon 390 of the MNX1 protein (p.Pro390Ala). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at