rs6840169
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001080506.3(TMEM150C):c.236-1162C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.907 in 152,278 control chromosomes in the GnomAD database, including 62,851 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 0.91 ( 62851 hom., cov: 32)
Consequence
TMEM150C
NM_001080506.3 intron
NM_001080506.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.209
Genes affected
TMEM150C (HGNC:37263): (transmembrane protein 150C) This gene encodes a transmembrane protein component of a mechanosensitve ion channel that is activated by mechanical stimuli in various cell types and confers slowly adapting, mechanically activated currents in dorsal root ganglion neurons. Mechanically activated ion channels are sensors that are critical for hearing, touch, pain, and blood pressure regulation. [provided by RefSeq, Jul 2017]
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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=-0.52).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TMEM150C | NM_001080506.3 | c.236-1162C>T | intron_variant | ENST00000449862.7 | |||
TMEM150C | NM_001353454.2 | c.326-1162C>T | intron_variant | ||||
TMEM150C | NM_001353455.2 | c.236-1162C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TMEM150C | ENST00000449862.7 | c.236-1162C>T | intron_variant | 1 | NM_001080506.3 | P1 | |||
TMEM150C | ENST00000508701.5 | c.236-1162C>T | intron_variant | 4 | |||||
TMEM150C | ENST00000515780.6 | c.236-1162C>T | intron_variant | 2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.907 AC: 138011AN: 152160Hom.: 62785 Cov.: 32
GnomAD3 genomes
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.907 AC: 138136AN: 152278Hom.: 62851 Cov.: 32 AF XY: 0.911 AC XY: 67820AN XY: 74450
GnomAD4 genome
?
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138136
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32
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67820
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74450
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3328
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3460
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