chr18-34978515-GGAAT-G
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Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 8P and 6B. PVS1BP6_ModerateBS2
The NM_001143827.3(MAPRE2):βc.2_5delβ(p.Met1_?2) variant causes a start lost, 5 prime UTR change. The variant allele was found at a frequency of 0.00164 in 1,551,538 control chromosomes in the GnomAD database, including 5 homozygotes. Variant has been reported in ClinVar as Likely benign (β ).
Frequency
Genomes: π 0.0017 ( 0 hom., cov: 33)
Exomes π: 0.0016 ( 5 hom. )
Consequence
MAPRE2
NM_001143827.3 start_lost, 5_prime_UTR
NM_001143827.3 start_lost, 5_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 3.59
Genes affected
MAPRE2 (HGNC:6891): (microtubule associated protein RP/EB family member 2) The protein encoded by this gene shares significant homology to the adenomatous polyposis coli (APC) protein-binding EB1 gene family. This protein is a microtubule-associated protein that is necessary for spindle symmetry during mitosis. It is thought to play a role in the tumorigenesis of colorectal cancers and the proliferative control of normal cells. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Jan 2012]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PVS1
Start lost variant, no new inframe start found.
BP6
Variant 18-34978515-GGAAT-G is Benign according to our data. Variant chr18-34978515-GGAAT-G is described in ClinVar as [Likely_benign]. Clinvar id is 2672722.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High AC in GnomAd4 at 254 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MAPRE2 | NM_001143827.3 | c.2_5del | p.Met1_?2 | start_lost, 5_prime_UTR_variant | 1/8 | ||
MAPRE2 | NM_001143826.3 | c.-70+1440_-70+1443del | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MAPRE2 | ENST00000436190.6 | c.2_5del | p.Met1_?2 | start_lost, 5_prime_UTR_variant | 1/8 | 2 | |||
MAPRE2 | ENST00000588349.6 | c.-69_-66del | 5_prime_UTR_variant | 1/5 | 5 | ||||
MAPRE2 | ENST00000413393.5 | c.-70+1440_-70+1443del | intron_variant | 5 | P4 |
Frequencies
GnomAD3 genomes AF: 0.00168 AC: 255AN: 152190Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.00129 AC: 199AN: 153868Hom.: 0 AF XY: 0.00124 AC XY: 101AN XY: 81672
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GnomAD4 exome AF: 0.00164 AC: 2295AN: 1399230Hom.: 5 AF XY: 0.00163 AC XY: 1126AN XY: 690148
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GnomAD4 genome AF: 0.00167 AC: 254AN: 152308Hom.: 0 Cov.: 33 AF XY: 0.00156 AC XY: 116AN XY: 74474
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Nov 01, 2023 | MAPRE2: BS1 - |
Computational scores
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at