rs12713828
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001058.4(TACR1):c.*478C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.393 in 155,870 control chromosomes in the GnomAD database, including 12,490 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 ( 12181 hom., cov: 32)
Exomes 𝑓: 0.37 ( 309 hom. )
Consequence
TACR1
NM_001058.4 3_prime_UTR
NM_001058.4 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.151
Genes affected
TACR1 (HGNC:11526): (tachykinin receptor 1) This gene belongs to a gene family of tachykinin receptors. These tachykinin receptors are characterized by interactions with G proteins and contain seven hydrophobic transmembrane regions. This gene encodes the receptor for the tachykinin substance P, also referred to as neurokinin 1. The encoded protein is also involved in the mediation of phosphatidylinositol metabolism of substance P. [provided by RefSeq, Sep 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=-0.82).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.435 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TACR1 | NM_001058.4 | c.*478C>T | 3_prime_UTR_variant | 5/5 | ENST00000305249.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TACR1 | ENST00000305249.10 | c.*478C>T | 3_prime_UTR_variant | 5/5 | 1 | NM_001058.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.394 AC: 59836AN: 151976Hom.: 12181 Cov.: 32
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GnomAD4 exome AF: 0.375 AC: 1415AN: 3778Hom.: 309 Cov.: 0 AF XY: 0.373 AC XY: 708AN XY: 1898
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GnomAD4 genome ? AF: 0.394 AC: 59854AN: 152092Hom.: 12181 Cov.: 32 AF XY: 0.388 AC XY: 28845AN XY: 74368
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ClinVar
Not reported inComputational 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