rs4629
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_ModerateBP7BA1
The ENST00000372555.8(TNNC2):c.384G>T(p.Thr128=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.518 in 1,613,748 control chromosomes in the GnomAD database, including 222,323 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 0.45 ( 16722 hom., cov: 31)
Exomes 𝑓: 0.53 ( 205601 hom. )
Consequence
TNNC2
ENST00000372555.8 synonymous
ENST00000372555.8 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -4.65
Genes affected
TNNC2 (HGNC:11944): (troponin C2, fast skeletal type) Troponin (Tn), a key protein complex in the regulation of striated muscle contraction, is composed of 3 subunits. The Tn-I subunit inhibits actomyosin ATPase, the Tn-T subunit binds tropomyosin and Tn-C, while the Tn-C subunit binds calcium and overcomes the inhibitory action of the troponin complex on actin filaments. The protein encoded by this gene is the Tn-C subunit. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.4).
BP7
Synonymous conserved (PhyloP=-4.65 with no splicing effect.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.539 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TNNC2 | NM_003279.3 | c.384G>T | p.Thr128= | synonymous_variant | 5/6 | ENST00000372555.8 | NP_003270.1 | |
TNNC2 | XM_011529031.3 | c.339G>T | p.Thr113= | synonymous_variant | 5/6 | XP_011527333.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TNNC2 | ENST00000372555.8 | c.384G>T | p.Thr128= | synonymous_variant | 5/6 | 1 | NM_003279.3 | ENSP00000361636 | P1 | |
TNNC2 | ENST00000372557.1 | c.339G>T | p.Thr113= | synonymous_variant | 6/7 | 3 | ENSP00000361638 |
Frequencies
GnomAD3 genomes AF: 0.449 AC: 68167AN: 151904Hom.: 16710 Cov.: 31
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GnomAD3 exomes AF: 0.503 AC: 126328AN: 251366Hom.: 33039 AF XY: 0.497 AC XY: 67470AN XY: 135876
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GnomAD4 exome AF: 0.526 AC: 768409AN: 1461726Hom.: 205601 Cov.: 62 AF XY: 0.521 AC XY: 378788AN XY: 727174
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GnomAD4 genome AF: 0.449 AC: 68195AN: 152022Hom.: 16722 Cov.: 31 AF XY: 0.449 AC XY: 33346AN XY: 74294
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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