rs548755417
Positions:
- chr7-157009949-AGCGGCGGCGGCGGCG-A
- chr7-157009949-AGCGGCGGCGGCGGCG-AGCG
- chr7-157009949-AGCGGCGGCGGCGGCG-AGCGGCG
- chr7-157009949-AGCGGCGGCGGCGGCG-AGCGGCGGCG
- chr7-157009949-AGCGGCGGCGGCGGCG-AGCGGCGGCGGCG
- chr7-157009949-AGCGGCGGCGGCGGCG-AGCGGCGGCGGCGGCGGCG
- chr7-157009949-AGCGGCGGCGGCGGCG-AGCGGCGGCGGCGGCGGCGGCG
- chr7-157009949-AGCGGCGGCGGCGGCG-AGCGGCGGCGGCGGCGGCGGCGGCG
- chr7-157009949-AGCGGCGGCGGCGGCG-AGCGGCGGCGGCGGCGGCGGCGGCGGCG
- chr7-157009949-AGCGGCGGCGGCGGCG-AGCGGCGGCGGCGGCGGCGGCGGCGGCGGCG
- chr7-157009949-AGCGGCGGCGGCGGCG-AGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCG
- chr7-157009949-AGCGGCGGCGGCGGCG-AGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCG
- chr7-157009949-AGCGGCGGCGGCGGCG-AGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCG
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP3BS2
The NM_005515.4(MNX1):c.387_401del(p.Ala130_Ala134del) variant causes a inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000661 in 908,254 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.0000077 ( 0 hom., cov: 0)
Exomes 𝑓: 0.0000064 ( 0 hom. )
Consequence
MNX1
NM_005515.4 inframe_deletion
NM_005515.4 inframe_deletion
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 3.14
Genes affected
MNX1 (HGNC:4979): (motor neuron and pancreas homeobox 1) This gene encodes a nuclear protein, which contains a homeobox domain and is a transcription factor. Mutations in this gene result in Currarino syndrome, an autosomic dominant congenital malformation. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2009]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
BP3
?
Nonframeshift variant in repetitive region in NM_005515.4
BS2
?
High AC in GnomAdExome4 at 5 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MNX1 | NM_005515.4 | c.387_401del | p.Ala130_Ala134del | inframe_deletion | 1/3 | ENST00000252971.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MNX1 | ENST00000252971.11 | c.387_401del | p.Ala130_Ala134del | inframe_deletion | 1/3 | 1 | NM_005515.4 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.00000771 AC: 1AN: 129766Hom.: 0 Cov.: 0
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GnomAD4 exome AF: 0.00000642 AC: 5AN: 778488Hom.: 0 AF XY: 0.00000550 AC XY: 2AN XY: 363726
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ClinVar
Not reported inComputational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at