chr7-97736303-T-C
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_003182.3(TAC1):c.294T>C(p.His98=) variant causes a synonymous change. The variant allele was found at a frequency of 0.000258 in 1,611,224 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 0.00029 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00025 ( 0 hom. )
Consequence
TAC1
NM_003182.3 synonymous
NM_003182.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 4.02
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 -10 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.47).
BP6
?
Variant 7-97736303-T-C is Benign according to our data. Variant chr7-97736303-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 741561.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
?
High AC in GnomAd at 44 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TAC1 | NM_003182.3 | c.294T>C | p.His98= | synonymous_variant | 6/7 | ENST00000319273.10 | |
TAC1 | NM_013997.3 | c.249T>C | p.His83= | synonymous_variant | 5/6 | ||
TAC1 | NM_013996.3 | c.289+1454T>C | intron_variant | ||||
TAC1 | NM_013998.3 | c.244+1454T>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TAC1 | ENST00000319273.10 | c.294T>C | p.His98= | synonymous_variant | 6/7 | 1 | NM_003182.3 | ||
TAC1 | ENST00000346867.4 | c.249T>C | p.His83= | synonymous_variant | 5/6 | 3 | P1 | ||
TAC1 | ENST00000350485.8 | c.289+1454T>C | intron_variant | 5 | |||||
TAC1 | ENST00000491437.1 | n.368T>C | non_coding_transcript_exon_variant | 3/4 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.000289 AC: 44AN: 152072Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000372 AC: 93AN: 250226Hom.: 0 AF XY: 0.000510 AC XY: 69AN XY: 135374
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GnomAD4 exome AF: 0.000255 AC: 372AN: 1459152Hom.: 0 Cov.: 29 AF XY: 0.000288 AC XY: 209AN XY: 725964
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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
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