rs1185888
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_016056.4(TMBIM4):c.97+2756C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.504 in 152,086 control chromosomes in the GnomAD database, including 20,638 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 0.50 ( 20638 hom., cov: 33)
Consequence
TMBIM4
NM_016056.4 intron
NM_016056.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.55
Genes affected
TMBIM4 (HGNC:24257): (transmembrane BAX inhibitor motif containing 4) Involved in negative regulation of apoptotic process and regulation of calcium-mediated signaling. Located in Golgi stack. [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=-0.93).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.771 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TMBIM4 | NM_016056.4 | c.97+2756C>T | intron_variant | ENST00000358230.8 | |||
TMBIM4 | NM_001282606.2 | c.97+2756C>T | intron_variant | ||||
TMBIM4 | NM_001282609.2 | c.97+2756C>T | intron_variant | ||||
TMBIM4 | NM_001282610.2 | c.42+2756C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TMBIM4 | ENST00000358230.8 | c.97+2756C>T | intron_variant | 1 | NM_016056.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.504 AC: 76620AN: 151968Hom.: 20616 Cov.: 33
GnomAD3 genomes
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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: 0.504 AC: 76686AN: 152086Hom.: 20638 Cov.: 33 AF XY: 0.507 AC XY: 37727AN XY: 74346
GnomAD4 genome
?
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76686
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33
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37727
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74346
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2212
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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