chr7-157005589-G-C
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The NM_005515.4(MNX1):c.1137C>G(p.Ala379=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000413 in 1,598,538 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.00027 ( 1 hom., cov: 33)
Exomes 𝑓: 0.000017 ( 1 hom. )
Consequence
MNX1
NM_005515.4 synonymous
NM_005515.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.257
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 -15 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.77).
BP6
?
Variant 7-157005589-G-C is Benign according to our data. Variant chr7-157005589-G-C is described in ClinVar as [Benign]. Clinvar id is 2066941.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-0.257 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.000269 (41/152208) while in subpopulation AFR AF= 0.000986 (41/41574). AF 95% confidence interval is 0.000747. There are 1 homozygotes in gnomad4. There are 22 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
High AC in GnomAd at 41 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MNX1 | NM_005515.4 | c.1137C>G | p.Ala379= | synonymous_variant | 3/3 | ENST00000252971.11 | |
MNX1 | NM_001165255.2 | c.501C>G | p.Ala167= | synonymous_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MNX1 | ENST00000252971.11 | c.1137C>G | p.Ala379= | synonymous_variant | 3/3 | 1 | NM_005515.4 | P2 | |
MNX1 | ENST00000543409.5 | c.501C>G | p.Ala167= | synonymous_variant | 3/3 | 1 | A2 | ||
MNX1 | ENST00000469500.5 | c.55+3409C>G | intron_variant | 1 | |||||
MNX1 | ENST00000479817.1 | c.38+4071C>G | intron_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.000270 AC: 41AN: 152100Hom.: 1 Cov.: 33
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GnomAD3 exomes AF: 0.0000318 AC: 7AN: 220266Hom.: 0 AF XY: 0.0000248 AC XY: 3AN XY: 121160
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GnomAD4 exome AF: 0.0000173 AC: 25AN: 1446330Hom.: 1 Cov.: 31 AF XY: 0.0000125 AC XY: 9AN XY: 718604
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 03, 2024 | - - |
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