NM_013251.4:c.114+200T>C
Variant names:
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_013251.4(TAC3):c.114+200T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00314 in 152,316 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0031 ( 4 hom., cov: 32)
Consequence
TAC3
NM_013251.4 intron
NM_013251.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.0880
Genes affected
TAC3 (HGNC:11521): (tachykinin precursor 3) This gene encodes a member of the tachykinin family of secreted neuropeptides. The encoded preproprotein is proteolytically processed to generate the mature peptide, which is primarily expressed in the central and peripheral nervous systems and functions as a neurotransmitter. This peptide is the ligand for the neurokinin-3 receptor. This protein is also expressed in the outer syncytiotrophoblast of the placenta and may be associated with pregnancy-induced hypertension and pre-eclampsia. Mutations in this gene are associated with normosmic hypogonadotropic hypogonadism. Alternative splicing results in multiple transcript variants, at least one of which encodes an isoform that is proteolytically processed. [provided by RefSeq, Feb 2016]
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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=-0.84).
BP6
Variant 12-57015484-A-G is Benign according to our data. Variant chr12-57015484-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 1187691.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High Homozygotes in GnomAd4 at 4 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TAC3 | NM_013251.4 | c.114+200T>C | intron_variant | Intron 2 of 6 | ENST00000458521.7 | NP_037383.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TAC3 | ENST00000458521.7 | c.114+200T>C | intron_variant | Intron 2 of 6 | 1 | NM_013251.4 | ENSP00000404056.2 | |||
TAC3 | ENST00000300108.7 | n.114+200T>C | intron_variant | Intron 2 of 8 | 2 | ENSP00000300108.3 | ||||
TAC3 | ENST00000379411.6 | n.114+200T>C | intron_variant | Intron 2 of 7 | 2 | ENSP00000368721.2 | ||||
TAC3 | ENST00000393867.5 | n.114+200T>C | intron_variant | Intron 2 of 9 | 2 | ENSP00000377445.1 |
Frequencies
GnomAD3 genomes AF: 0.00312 AC: 475AN: 152198Hom.: 4 Cov.: 32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.00314 AC: 479AN: 152316Hom.: 4 Cov.: 32 AF XY: 0.00286 AC XY: 213AN XY: 74480
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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
Apr 16, 2019
GeneDx
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
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Computational scores
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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