rs11283943
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.
The NM_001085377.2(MCC):c.1925+5_1925+6insAAGACAGTGCGAGG variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00015 in 1,610,664 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 0.00013 ( 0 hom., cov: 0)
Exomes 𝑓: 0.00015 ( 0 hom. )
Consequence
MCC
NM_001085377.2 splice_region, intron
NM_001085377.2 splice_region, intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.14
Genes affected
MCC (HGNC:6935): (MCC regulator of WNT signaling pathway) This gene is a candidate colorectal tumor suppressor gene that is thought to negatively regulate cell cycle progression. The orthologous gene in the mouse expresses a phosphoprotein associated with the plasma membrane and membrane organelles, and overexpression of the mouse protein inhibits entry into S phase. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MCC | NM_001085377.2 | c.1925+5_1925+6insAAGACAGTGCGAGG | splice_region_variant, intron_variant | Intron 12 of 18 | ENST00000408903.7 | NP_001078846.2 | ||
MCC | NM_002387.3 | c.1355+5_1355+6insAAGACAGTGCGAGG | splice_region_variant, intron_variant | Intron 10 of 16 | NP_002378.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MCC | ENST00000408903.7 | c.1925+5_1925+6insAAGACAGTGCGAGG | splice_region_variant, intron_variant | Intron 12 of 18 | 2 | NM_001085377.2 | ENSP00000386227.3 | |||
MCC | ENST00000302475.9 | c.1355+5_1355+6insAAGACAGTGCGAGG | splice_region_variant, intron_variant | Intron 10 of 16 | 1 | ENSP00000305617.4 | ||||
MCC | ENST00000515367.6 | c.1166+5_1166+6insAAGACAGTGCGAGG | splice_region_variant, intron_variant | Intron 10 of 16 | 5 | ENSP00000421615.2 | ||||
MCC | ENST00000514701.5 | c.1355+5_1355+6insAAGACAGTGCGAGG | splice_region_variant, intron_variant | Intron 10 of 13 | 2 | ENSP00000485220.1 |
Frequencies
GnomAD3 genomes AF: 0.000125 AC: 19AN: 151824Hom.: 0 Cov.: 0 show subpopulations
GnomAD3 genomes
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GnomAD2 exomes AF: 0.000338 AC: 82AN: 242414 AF XY: 0.000374 show subpopulations
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GnomAD4 exome AF: 0.000153 AC: 223AN: 1458722Hom.: 0 Cov.: 35 AF XY: 0.000160 AC XY: 116AN XY: 725516 show subpopulations
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223
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44442
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26064
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216
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39592
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85572
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53334
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1110374
Gnomad4 Remaining exome
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5
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60260
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GnomAD4 genome AF: 0.000125 AC: 19AN: 151942Hom.: 0 Cov.: 0 AF XY: 0.000148 AC XY: 11AN XY: 74242 show subpopulations
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ClinVar
Not reported inComputational scores
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Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at