rs11237828
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001098816.3(TENM4):c.-321+18333A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.22 in 153,328 control chromosomes in the GnomAD database, including 3,948 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 0.22 ( 3922 hom., cov: 30)
Exomes 𝑓: 0.14 ( 26 hom. )
Consequence
TENM4
NM_001098816.3 intron
NM_001098816.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0820
Genes affected
TENM4 (HGNC:29945): (teneurin transmembrane protein 4) The protein encoded by this gene plays a role in establishing proper neuronal connectivity during development. Defects in this gene have been associated with hereditary essential tremor-5. [provided by RefSeq, Oct 2016]
MIR5579 (HGNC:43485): (microRNA 5579) microRNAs (miRNAs) are short (20-24 nt) non-coding RNAs that are involved in post-transcriptional regulation of gene expression in multicellular organisms by affecting both the stability and translation of mRNAs. miRNAs are transcribed by RNA polymerase II as part of capped and polyadenylated primary transcripts (pri-miRNAs) that can be either protein-coding or non-coding. The primary transcript is cleaved by the Drosha ribonuclease III enzyme to produce an approximately 70-nt stem-loop precursor miRNA (pre-miRNA), which is further cleaved by the cytoplasmic Dicer ribonuclease to generate the mature miRNA and antisense miRNA star (miRNA*) products. The mature miRNA is incorporated into a RNA-induced silencing complex (RISC), which recognizes target mRNAs through imperfect base pairing with the miRNA and most commonly results in translational inhibition or destabilization of the target mRNA. The RefSeq represents the predicted microRNA stem-loop. [provided by RefSeq, Sep 2009]
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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=-0.9).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.346 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TENM4 | NM_001098816.3 | c.-321+18333A>G | intron_variant | ENST00000278550.12 | |||
MIR5579 | NR_049841.1 | n.51A>G | non_coding_transcript_exon_variant | 1/1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TENM4 | ENST00000278550.12 | c.-321+18333A>G | intron_variant | 5 | NM_001098816.3 | P1 | |||
MIR5579 | ENST00000580400.1 | n.51A>G | mature_miRNA_variant | 1/1 | |||||
TENM4 | ENST00000528688.5 | n.239+16786A>G | intron_variant, non_coding_transcript_variant | 3 | |||||
TENM4 | ENST00000531583.1 | n.440+18333A>G | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.221 AC: 33482AN: 151312Hom.: 3922 Cov.: 30
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GnomAD3 exomes AF: 0.122 AC: 9AN: 74Hom.: 1 AF XY: 0.0333 AC XY: 1AN XY: 30
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GnomAD4 exome AF: 0.136 AC: 259AN: 1898Hom.: 26 Cov.: 0 AF XY: 0.149 AC XY: 143AN XY: 962
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GnomAD4 genome ? AF: 0.221 AC: 33522AN: 151430Hom.: 3922 Cov.: 30 AF XY: 0.220 AC XY: 16299AN XY: 73950
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ClinVar
Not reported inComputational 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
Find out detailed SpliceAI scores and Pangolin per-transcript scores at