rs512398
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001098816.3(TENM4):c.-320-36181A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.424 in 152,114 control chromosomes in the GnomAD database, including 13,967 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 0.42 ( 13967 hom., cov: 33)
Consequence
TENM4
NM_001098816.3 intron
NM_001098816.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.226
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]
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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=-0.91).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.589 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TENM4 | NM_001098816.3 | c.-320-36181A>G | intron_variant | ENST00000278550.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TENM4 | ENST00000278550.12 | c.-320-36181A>G | intron_variant | 5 | NM_001098816.3 | P1 | |||
TENM4 | ENST00000528688.5 | n.240-36181A>G | intron_variant, non_coding_transcript_variant | 3 | |||||
TENM4 | ENST00000531583.1 | n.441-36181A>G | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.424 AC: 64478AN: 151996Hom.: 13954 Cov.: 33
GnomAD3 genomes
?
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64478
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151996
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33
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.424 AC: 64523AN: 152114Hom.: 13967 Cov.: 33 AF XY: 0.426 AC XY: 31642AN XY: 74354
GnomAD4 genome
?
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AC:
64523
AN:
152114
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33
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31642
AN XY:
74354
Gnomad4 AFR
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1595
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
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