7-157005513-G-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_005515.4(MNX1):c.*7C>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00015 in 1,445,424 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
Genomes: 𝑓 0.00066 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000090 ( 0 hom. )
Consequence
MNX1
NM_005515.4 3_prime_UTR
NM_005515.4 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.0490
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 Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.73).
BP6
?
Variant 7-157005513-G-C is Benign according to our data. Variant chr7-157005513-G-C is described in ClinVar as [Likely_benign]. Clinvar id is 3040501.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.000665 (101/151966) while in subpopulation AFR AF= 0.00234 (97/41526). AF 95% confidence interval is 0.00196. There are 0 homozygotes in gnomad4. There are 49 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
High AC in GnomAd at 101 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MNX1 | NM_005515.4 | c.*7C>G | 3_prime_UTR_variant | 3/3 | ENST00000252971.11 | ||
MNX1 | NM_001165255.2 | c.*7C>G | 3_prime_UTR_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MNX1 | ENST00000252971.11 | c.*7C>G | 3_prime_UTR_variant | 3/3 | 1 | NM_005515.4 | P2 | ||
MNX1 | ENST00000543409.5 | c.*7C>G | 3_prime_UTR_variant | 3/3 | 1 | A2 | |||
MNX1 | ENST00000469500.5 | c.55+3485C>G | intron_variant | 1 | |||||
MNX1 | ENST00000479817.1 | c.38+4147C>G | intron_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.000665 AC: 101AN: 151862Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.000114 AC: 7AN: 61504Hom.: 0 AF XY: 0.0000280 AC XY: 1AN XY: 35684
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GnomAD4 exome AF: 0.0000897 AC: 116AN: 1293458Hom.: 0 Cov.: 30 AF XY: 0.0000803 AC XY: 51AN XY: 634874
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
MNX1-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Sep 11, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at