rs10101155
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_007332.3(TRPA1):c.945-344G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.392 in 151,918 control chromosomes in the GnomAD database, including 12,294 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 0.39 ( 12294 hom., cov: 32)
Consequence
TRPA1
NM_007332.3 intron
NM_007332.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.24
Genes affected
TRPA1 (HGNC:497): (transient receptor potential cation channel subfamily A member 1) The structure of the protein encoded by this gene is highly related to both the protein ankyrin and transmembrane proteins. The specific function of this protein has not yet been determined; however, studies indicate the function may involve a role in signal transduction and growth control. [provided by RefSeq, Jul 2008]
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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=-0.97).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.613 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TRPA1 | NM_007332.3 | c.945-344G>T | intron_variant | ENST00000262209.5 | |||
TRPA1 | XM_011517624.3 | c.1020-344G>T | intron_variant | ||||
TRPA1 | XM_011517625.3 | c.945-344G>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRPA1 | ENST00000262209.5 | c.945-344G>T | intron_variant | 1 | NM_007332.3 | P1 | |||
MSC-AS1 | ENST00000518916.5 | n.469+7166C>A | intron_variant, non_coding_transcript_variant | 3 | |||||
TRPA1 | ENST00000523582.5 | c.501-344G>T | intron_variant | 5 | |||||
MSC-AS1 | ENST00000519068.3 | n.449-581C>A | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.391 AC: 59412AN: 151800Hom.: 12264 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: 0.392 AC: 59483AN: 151918Hom.: 12294 Cov.: 32 AF XY: 0.398 AC XY: 29543AN XY: 74254
GnomAD4 genome
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151918
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32
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29543
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74254
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1916
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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