chr5-168062044-C-CTT
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1
The NM_001395460.1(TENM2):c.1310-5_1310-4dup variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.085 ( 662 hom., cov: 0)
Exomes 𝑓: 0.11 ( 434 hom. )
Consequence
TENM2
NM_001395460.1 splice_polypyrimidine_tract, intron
NM_001395460.1 splice_polypyrimidine_tract, intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.806
Genes affected
TENM2 (HGNC:29943): (teneurin transmembrane protein 2) Enables cell adhesion molecule binding activity and signaling receptor binding activity. Involved in several processes, including calcium-mediated signaling using intracellular calcium source; heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules; and retrograde trans-synaptic signaling by trans-synaptic protein complex. Located in cell-cell junction and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP6
?
Variant 5-168062044-C-CTT is Benign according to our data. Variant chr5-168062044-C-CTT is described in ClinVar as [Benign]. Clinvar id is 403528.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.151 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TENM2 | NM_001395460.1 | c.1310-5_1310-4dup | splice_polypyrimidine_tract_variant, intron_variant | ENST00000518659.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TENM2 | ENST00000518659.6 | c.1310-5_1310-4dup | splice_polypyrimidine_tract_variant, intron_variant | 5 | NM_001395460.1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0855 AC: 12563AN: 147002Hom.: 664 Cov.: 0
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GnomAD4 exome AF: 0.108 AC: 140929AN: 1302388Hom.: 434 Cov.: 0 AF XY: 0.109 AC XY: 70613AN XY: 647566
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GnomAD4 genome ? AF: 0.0854 AC: 12552AN: 147052Hom.: 662 Cov.: 0 AF XY: 0.0863 AC XY: 6157AN XY: 71332
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Mar 28, 2016 | Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: 8.2% of total chromosomes in ExAC - |
Computational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at