NM_152263.4:c.92A>C
Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 3P and 20B. PM1PP2BP4_StrongBP6_Very_StrongBS1BS2
The NM_152263.4(TPM3):āc.92A>Cā(p.Lys31Thr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00102 in 1,613,868 control chromosomes in the GnomAD database, including 18 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ).
Frequency
Consequence
NM_152263.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -17 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00546 AC: 831AN: 152218Hom.: 12 Cov.: 31
GnomAD3 exomes AF: 0.00132 AC: 330AN: 249372Hom.: 4 AF XY: 0.000990 AC XY: 134AN XY: 135320
GnomAD4 exome AF: 0.000553 AC: 808AN: 1461532Hom.: 6 Cov.: 31 AF XY: 0.000462 AC XY: 336AN XY: 727104
GnomAD4 genome AF: 0.00547 AC: 833AN: 152336Hom.: 12 Cov.: 31 AF XY: 0.00540 AC XY: 402AN XY: 74496
ClinVar
Submissions by phenotype
not provided Benign:3
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not specified Benign:2
Lys31Thr in exon 1 of TPM3: This variant is not expected to have clinical signif icance because it has been identified in 1.9% (81/4196) of African American chro mosomes from a broad population by the NHLBI Exome Sequencing Project (http://ev s.gs.washington.edu/EVS; dbSNP rs62000429). -
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TPM3-related disorder Benign:1
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Congenital myopathy with fiber type disproportion;C5829889:Congenital myopathy 4B, autosomal recessive Benign:1
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Congenital myopathy with fiber type disproportion Benign:1
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
Congenital myopathy 4B, autosomal recessive Benign:1
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at