rs2228359
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1
The NM_003285.3(TNR):āc.3237T>Cā(p.Asp1079=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.688 in 1,613,486 control chromosomes in the GnomAD database, including 383,955 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: š 0.65 ( 32655 hom., cov: 32)
Exomes š: 0.69 ( 351300 hom. )
Consequence
TNR
NM_003285.3 synonymous
NM_003285.3 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.951
Genes affected
TNR (HGNC:11953): (tenascin R) This gene encodes a member of the tenascin family of extracellular matrix glycoproteins. The encoded protein is restricted to the central nervous system. The protein may play a role in neurite outgrowth, neural cell adhesion and modulation of sodium channel function. It is a constituent of perineuronal nets. [provided by RefSeq, Aug 2013]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.57).
BP7
?
Synonymous conserved (PhyloP=0.951 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.786 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TNR | NM_003285.3 | c.3237T>C | p.Asp1079= | synonymous_variant | 17/23 | ENST00000367674.7 | |
TNR | NM_001328635.2 | c.2238T>C | p.Asp746= | synonymous_variant | 17/23 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TNR | ENST00000367674.7 | c.3237T>C | p.Asp1079= | synonymous_variant | 17/23 | 5 | NM_003285.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.650 AC: 98752AN: 151938Hom.: 32628 Cov.: 32
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GnomAD3 exomes AF: 0.697 AC: 174673AN: 250766Hom.: 61435 AF XY: 0.695 AC XY: 94206AN XY: 135482
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GnomAD4 exome AF: 0.692 AC: 1011000AN: 1461430Hom.: 351300 Cov.: 57 AF XY: 0.691 AC XY: 502577AN XY: 726998
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GnomAD4 genome ? AF: 0.650 AC: 98828AN: 152056Hom.: 32655 Cov.: 32 AF XY: 0.655 AC XY: 48677AN XY: 74328
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at