7-97732472-C-T
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_003182.3(TAC1):c.-9-132C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.515 in 1,053,232 control chromosomes in the GnomAD database, including 142,997 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 0.55 ( 23786 hom., cov: 31)
Exomes 𝑓: 0.51 ( 119211 hom. )
Consequence
TAC1
NM_003182.3 intron
NM_003182.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.156
Genes affected
TAC1 (HGNC:11517): (tachykinin precursor 1) This gene encodes four products of the tachykinin peptide hormone family, substance P and neurokinin A, as well as the related peptides, neuropeptide K and neuropeptide gamma. These hormones are thought to function as neurotransmitters which interact with nerve receptors and smooth muscle cells. They are known to induce behavioral responses and function as vasodilators and secretagogues. Substance P is an antimicrobial peptide with antibacterial and antifungal properties. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Nov 2014]
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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=-0.8).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.68 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TAC1 | NM_003182.3 | c.-9-132C>T | intron_variant | ENST00000319273.10 | |||
TAC1 | NM_013996.3 | c.-9-132C>T | intron_variant | ||||
TAC1 | NM_013997.3 | c.-9-132C>T | intron_variant | ||||
TAC1 | NM_013998.3 | c.-9-132C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TAC1 | ENST00000319273.10 | c.-9-132C>T | intron_variant | 1 | NM_003182.3 | ||||
TAC1 | ENST00000346867.4 | c.-9-132C>T | intron_variant | 3 | P1 | ||||
TAC1 | ENST00000350485.8 | c.-9-132C>T | intron_variant | 5 | |||||
TAC1 | ENST00000495916.1 | n.36-132C>T | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.552 AC: 83766AN: 151826Hom.: 23755 Cov.: 31
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GnomAD4 exome AF: 0.509 AC: 458470AN: 901286Hom.: 119211 AF XY: 0.508 AC XY: 234411AN XY: 461202
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GnomAD4 genome AF: 0.552 AC: 83858AN: 151946Hom.: 23786 Cov.: 31 AF XY: 0.549 AC XY: 40766AN XY: 74272
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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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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at