7-157005556-C-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_005515.4(MNX1):c.1170G>A(p.Pro390Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000713 in 1,402,060 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 Likely benign (★).
Frequency
Consequence
NM_005515.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MNX1 | ENST00000252971.11 | c.1170G>A | p.Pro390Pro | synonymous_variant | Exon 3 of 3 | 1 | NM_005515.4 | ENSP00000252971.5 | ||
MNX1 | ENST00000543409.5 | c.534G>A | p.Pro178Pro | synonymous_variant | Exon 3 of 3 | 1 | ENSP00000438552.1 | |||
MNX1 | ENST00000469500.5 | c.55+3442G>A | intron_variant | Intron 1 of 1 | 1 | ENSP00000475129.1 | ||||
MNX1 | ENST00000479817.1 | c.37+4104G>A | intron_variant | Intron 1 of 1 | 1 | ENSP00000474286.1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome AF: 7.13e-7 AC: 1AN: 1402060Hom.: 0 Cov.: 31 AF XY: 0.00000144 AC XY: 1AN XY: 694410
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.