rs3748172
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Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_002160.4(TNC):c.3165C>T(p.Ala1055Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0122 in 1,614,102 control chromosomes in the GnomAD database, including 852 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.016 ( 114 hom., cov: 32)
Exomes 𝑓: 0.012 ( 738 hom. )
Consequence
TNC
NM_002160.4 synonymous
NM_002160.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -5.43
Genes affected
TNC (HGNC:5318): (tenascin C) This gene encodes an extracellular matrix protein with a spatially and temporally restricted tissue distribution. This protein is homohexameric with disulfide-linked subunits, and contains multiple EGF-like and fibronectin type-III domains. It is implicated in guidance of migrating neurons as well as axons during development, synaptic plasticity, and neuronal regeneration. [provided by RefSeq, Jul 2011]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -21 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.68).
BP6
Variant 9-115073652-G-A is Benign according to our data. Variant chr9-115073652-G-A is described in ClinVar as [Benign]. Clinvar id is 586834.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=-5.43 with no splicing effect.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0996 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TNC | NM_002160.4 | c.3165C>T | p.Ala1055Ala | synonymous_variant | 10/28 | ENST00000350763.9 | NP_002151.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TNC | ENST00000350763.9 | c.3165C>T | p.Ala1055Ala | synonymous_variant | 10/28 | 1 | NM_002160.4 | ENSP00000265131.4 |
Frequencies
GnomAD3 genomes AF: 0.0163 AC: 2479AN: 152116Hom.: 111 Cov.: 32
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GnomAD3 exomes AF: 0.0333 AC: 8344AN: 250572Hom.: 440 AF XY: 0.0311 AC XY: 4216AN XY: 135476
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GnomAD4 exome AF: 0.0117 AC: 17166AN: 1461868Hom.: 738 Cov.: 32 AF XY: 0.0127 AC XY: 9215AN XY: 727240
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GnomAD4 genome AF: 0.0164 AC: 2490AN: 152234Hom.: 114 Cov.: 32 AF XY: 0.0198 AC XY: 1472AN XY: 74450
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ClinVar
Significance: Benign
Submissions summary: Benign:4
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:3
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Aug 10, 2018 | - - |
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Dec 12, 2018 | - - |
Autosomal dominant nonsyndromic hearing loss 56 Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Mar 15, 2022 | - - |
Computational scores
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BayesDel_noAF
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CADD
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DANN
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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