rs3735943
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Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1
The NM_007332.3(TRPA1):c.1630C>T(p.Leu544=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.51 in 1,609,828 control chromosomes in the GnomAD database, including 212,152 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.52 ( 20935 hom., cov: 32)
Exomes 𝑓: 0.51 ( 191217 hom. )
Consequence
TRPA1
NM_007332.3 synonymous
NM_007332.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.73
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 -15 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.79).
BP6
?
Variant 8-72053767-G-A is Benign according to our data. Variant chr8-72053767-G-A is described in ClinVar as [Benign]. Clinvar id is 1342282.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=1.73 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.673 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TRPA1 | NM_007332.3 | c.1630C>T | p.Leu544= | synonymous_variant | 13/27 | ENST00000262209.5 | |
MSC-AS1 | NR_033652.1 | n.2257G>A | non_coding_transcript_exon_variant | 5/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRPA1 | ENST00000262209.5 | c.1630C>T | p.Leu544= | synonymous_variant | 13/27 | 1 | NM_007332.3 | P1 | |
MSC-AS1 | ENST00000518916.5 | n.469+1151G>A | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.519 AC: 78883AN: 151914Hom.: 20901 Cov.: 32
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GnomAD3 exomes AF: 0.554 AC: 138305AN: 249818Hom.: 39427 AF XY: 0.545 AC XY: 73531AN XY: 134960
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GnomAD4 exome AF: 0.509 AC: 741460AN: 1457796Hom.: 191217 Cov.: 34 AF XY: 0.508 AC XY: 368715AN XY: 725228
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GnomAD4 genome ? AF: 0.519 AC: 78966AN: 152032Hom.: 20935 Cov.: 32 AF XY: 0.524 AC XY: 38936AN XY: 74316
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Familial episodic pain syndrome with predominantly upper body involvement Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Sep 10, 2021 | - - |
Computational scores
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Name
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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