9-35682299-T-C
Variant names:
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_213674.1(TPM2):c.773-136A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000364 in 1,044,780 control chromosomes in the GnomAD database, including 1 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 0.000046 ( 0 hom., cov: 31)
Exomes 𝑓: 0.000035 ( 1 hom. )
Consequence
TPM2
NM_213674.1 intron
NM_213674.1 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.830
Genes affected
TPM2 (HGNC:12011): (tropomyosin 2) This gene encodes beta-tropomyosin, a member of the actin filament binding protein family, and mainly expressed in slow, type 1 muscle fibers. Mutations in this gene can alter the expression of other sarcomeric tropomyosin proteins, and cause cap disease, nemaline myopathy and distal arthrogryposis syndromes. Alternatively spliced transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Mar 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BS2
High AC in GnomAd4 at 7 AD gene.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TPM2 | ENST00000378292.9 | c.773-136A>G | intron_variant | Intron 8 of 8 | 1 | ENSP00000367542.3 | ||||
TPM2 | ENST00000644325 | c.*409A>G | 3_prime_UTR_variant | Exon 4 of 4 | ENSP00000495075.1 | |||||
TPM2 | ENST00000329305.6 | c.773-136A>G | intron_variant | Intron 8 of 8 | 2 | ENSP00000367541.1 | ||||
TPM2 | ENST00000643485.1 | n.1550A>G | non_coding_transcript_exon_variant | Exon 8 of 8 |
Frequencies
GnomAD3 genomes AF: 0.0000461 AC: 7AN: 151926Hom.: 0 Cov.: 31
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GnomAD4 exome AF: 0.0000347 AC: 31AN: 892854Hom.: 1 Cov.: 12 AF XY: 0.0000392 AC XY: 18AN XY: 458764
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GnomAD4 genome AF: 0.0000461 AC: 7AN: 151926Hom.: 0 Cov.: 31 AF XY: 0.0000404 AC XY: 3AN XY: 74196
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ClinVar
Not reported inComputational scores
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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