7-157009949-AGCGGCGGCGGCGGCG-AGCGGCG
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Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP3BP6_Very_StrongBS1BS2
The NM_005515.4(MNX1):c.393_401delCGCCGCCGC(p.Ala132_Ala134del) variant causes a disruptive inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000166 in 908,220 control chromosomes in the GnomAD database, including 1 homozygotes. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.00018 ( 0 hom., cov: 0)
Exomes 𝑓: 0.00016 ( 1 hom. )
Consequence
MNX1
NM_005515.4 disruptive_inframe_deletion
NM_005515.4 disruptive_inframe_deletion
Scores
Not classified
Clinical Significance
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 Benign. Variant got -17 ACMG points.
BP3
Nonframeshift variant in repetitive region in NM_005515.4
BP6
Variant 7-157009949-AGCGGCGGCG-A is Benign according to our data. Variant chr7-157009949-AGCGGCGGCG-A is described in ClinVar as [Likely_benign]. Clinvar id is 1651300.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS1
Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.000185 (24/129774) while in subpopulation EAS AF= 0.00193 (8/4146). AF 95% confidence interval is 0.000959. There are 0 homozygotes in gnomad4. There are 7 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.
BS2
High AC in GnomAd4 at 24 AD gene.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000185 AC: 24AN: 129766Hom.: 0 Cov.: 0
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GnomAD4 exome AF: 0.000163 AC: 127AN: 778446Hom.: 1 AF XY: 0.000124 AC XY: 45AN XY: 363696
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GnomAD4 genome AF: 0.000185 AC: 24AN: 129774Hom.: 0 Cov.: 0 AF XY: 0.000111 AC XY: 7AN XY: 62922
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ClinVar
Significance: Likely benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 24, 2024 | - - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Aug 01, 2023 | MNX1: PM4, BS1, BS2 - |
Currarino triad Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Oct 28, 2021 | - - |
Computational scores
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at