rs1862198
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001395460.1(TENM2):c.712+117G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.815 in 829,332 control chromosomes in the GnomAD database, including 280,952 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.72 ( 42613 hom., cov: 31)
Exomes 𝑓: 0.83 ( 238339 hom. )
Consequence
TENM2
NM_001395460.1 intron
NM_001395460.1 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.374
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 -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.94).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.958 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TENM2 | NM_001395460.1 | c.712+117G>A | intron_variant | ENST00000518659.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TENM2 | ENST00000518659.6 | c.712+117G>A | intron_variant | 5 | NM_001395460.1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.725 AC: 110157AN: 151906Hom.: 42590 Cov.: 31
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GnomAD4 exome AF: 0.835 AC: 565481AN: 677308Hom.: 238339 AF XY: 0.839 AC XY: 294953AN XY: 351502
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GnomAD4 genome ? AF: 0.725 AC: 110215AN: 152024Hom.: 42613 Cov.: 31 AF XY: 0.732 AC XY: 54415AN XY: 74292
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at