rs62063845
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Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1
The ENST00000262410.10(MAPT):c.1732+2342T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.19 in 1,571,794 control chromosomes in the GnomAD database, including 32,173 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.14 ( 2142 hom., cov: 33)
Exomes 𝑓: 0.19 ( 30031 hom. )
Consequence
MAPT
ENST00000262410.10 intron
ENST00000262410.10 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.732
Genes affected
MAPT (HGNC:6893): (microtubule associated protein tau) This gene encodes the microtubule-associated protein tau (MAPT) whose transcript undergoes complex, regulated alternative splicing, giving rise to several mRNA species. MAPT transcripts are differentially expressed in the nervous system, depending on stage of neuronal maturation and neuron type. MAPT gene mutations have been associated with several neurodegenerative disorders such as Alzheimer's disease, Pick's disease, frontotemporal dementia, cortico-basal degeneration and progressive supranuclear palsy. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -16 ACMG points.
BP6
Variant 17-45993928-T-C is Benign according to our data. Variant chr17-45993928-T-C is described in ClinVar as [Benign]. Clinvar id is 98206.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-45993928-T-C is described in Lovd as [Benign].
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.214 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MAPT | NM_001377265.1 | c.1732+2342T>C | intron_variant | ENST00000262410.10 | NP_001364194.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MAPT | ENST00000262410.10 | c.1732+2342T>C | intron_variant | 1 | NM_001377265.1 | ENSP00000262410 | A2 |
Frequencies
GnomAD3 genomes AF: 0.145 AC: 22072AN: 152134Hom.: 2144 Cov.: 33
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GnomAD3 exomes AF: 0.145 AC: 27044AN: 186804Hom.: 2576 AF XY: 0.147 AC XY: 14803AN XY: 100560
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GnomAD4 exome AF: 0.195 AC: 276451AN: 1419542Hom.: 30031 Cov.: 33 AF XY: 0.192 AC XY: 135004AN XY: 702404
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GnomAD4 genome AF: 0.145 AC: 22062AN: 152252Hom.: 2142 Cov.: 33 AF XY: 0.136 AC XY: 10120AN XY: 74454
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ClinVar
Significance: Benign
Submissions summary: Benign:7Other:1
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:4
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Benign, no assertion criteria provided | clinical testing | Genome Diagnostics Laboratory, University Medical Center Utrecht | - | - - |
Benign, no assertion criteria provided | clinical testing | Clinical Genetics, Academic Medical Center | - | - - |
Benign, no assertion criteria provided | clinical testing | Genome Diagnostics Laboratory, Amsterdam University Medical Center | - | - - |
not provided Benign:2Other:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Aug 11, 2018 | - - |
not provided, no classification provided | literature only | VIB Department of Molecular Genetics, University of Antwerp | - | - - |
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Frontotemporal dementia Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 15, 2024 | - - |
Computational scores
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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
DS_DG_spliceai
Position offset: 49
Find out detailed SpliceAI scores and Pangolin per-transcript scores at