17-3510866-T-C
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_145068.4(TRPV3):c.*3051A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.346 in 152,278 control chromosomes in the GnomAD database, including 10,800 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.35 ( 10798 hom., cov: 33)
Exomes 𝑓: 0.47 ( 2 hom. )
Consequence
TRPV3
NM_145068.4 3_prime_UTR
NM_145068.4 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.804
Genes affected
TRPV3 (HGNC:18084): (transient receptor potential cation channel subfamily V member 3) This gene product belongs to a family of nonselective cation channels that function in a variety of processes, including temperature sensation and vasoregulation. The thermosensitive members of this family are expressed in subsets of sensory neurons that terminate in the skin, and are activated at distinct physiological temperatures. This channel is activated at temperatures between 22 and 40 degrees C. This gene lies in close proximity to another family member gene on chromosome 17, and the two encoded proteins are thought to associate with each other to form heteromeric channels. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Apr 2012]
SPATA22 (HGNC:30705): (spermatogenesis associated 22) Predicted to be involved in regulation of meiotic cell cycle. Predicted to act upstream of or within several processes, including fertilization; gamete generation; and meiosis I cell cycle process. Predicted to be located in chromosome. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.81).
BP6
Variant 17-3510866-T-C is Benign according to our data. Variant chr17-3510866-T-C is described in ClinVar as [Benign]. Clinvar id is 322682.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.622 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TRPV3 | NM_145068.4 | c.*3051A>G | 3_prime_UTR_variant | 18/18 | ENST00000576742.6 | NP_659505.1 | ||
TRPV3 | NM_001258205.2 | c.*3051A>G | 3_prime_UTR_variant | 18/18 | NP_001245134.1 | |||
SPATA22 | NM_001321337.2 | c.-74+2546A>G | intron_variant | NP_001308266.1 | ||||
SPATA22 | NM_001321336.2 | c.-74+2546A>G | intron_variant | NP_001308265.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TRPV3 | ENST00000576742.6 | c.*3051A>G | 3_prime_UTR_variant | 18/18 | 1 | NM_145068.4 | ENSP00000461518.2 |
Frequencies
GnomAD3 genomes AF: 0.346 AC: 52683AN: 152130Hom.: 10786 Cov.: 33
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GnomAD4 exome AF: 0.467 AC: 14AN: 30Hom.: 2 Cov.: 0 AF XY: 0.500 AC XY: 11AN XY: 22
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GnomAD4 genome AF: 0.346 AC: 52699AN: 152248Hom.: 10798 Cov.: 33 AF XY: 0.359 AC XY: 26702AN XY: 74440
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Isolated focal non-epidermolytic palmoplantar keratoderma Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 12, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. - |
not provided Benign:1
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at