chr17-3583394-G-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_ModerateBP6_Moderate
The NM_080704.4(TRPV1):c.1420C>A(p.Arg474=) variant causes a synonymous change. The variant allele was found at a frequency of 0.00000186 in 1,609,812 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000013 ( 0 hom., cov: 32)
Exomes 𝑓: 6.9e-7 ( 0 hom. )
Consequence
TRPV1
NM_080704.4 synonymous
NM_080704.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 4.52
Genes affected
TRPV1 (HGNC:12716): (transient receptor potential cation channel subfamily V member 1) Capsaicin, the main pungent ingredient in hot chili peppers, elicits a sensation of burning pain by selectively activating sensory neurons that convey information about noxious stimuli to the central nervous system. The protein encoded by this gene is a receptor for capsaicin and is a non-selective cation channel that is structurally related to members of the TRP family of ion channels. This receptor is also activated by increases in temperature in the noxious range, suggesting that it functions as a transducer of painful thermal stimuli in vivo. Four transcript variants encoding the same protein, but with different 5' UTR sequence, have been described for this gene. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.3).
BP6
?
Variant 17-3583394-G-T is Benign according to our data. Variant chr17-3583394-G-T is described in ClinVar as [Likely_benign]. Clinvar id is 743037.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TRPV1 | NM_080704.4 | c.1420C>A | p.Arg474= | synonymous_variant | 10/17 | ENST00000572705.2 | |
TRPV1 | NM_018727.5 | c.1420C>A | p.Arg474= | synonymous_variant | 9/16 | ||
TRPV1 | NM_080705.4 | c.1420C>A | p.Arg474= | synonymous_variant | 9/16 | ||
TRPV1 | NM_080706.3 | c.1420C>A | p.Arg474= | synonymous_variant | 8/15 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRPV1 | ENST00000572705.2 | c.1420C>A | p.Arg474= | synonymous_variant | 10/17 | 1 | NM_080704.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152224Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.00000414 AC: 1AN: 241548Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 130680
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GnomAD4 exome AF: 6.86e-7 AC: 1AN: 1457588Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 724496
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GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152224Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74360
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Aug 15, 2018 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
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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