chr9-35683151-C-T
Variant summary
Our verdict is Benign. Variant got -18 ACMG points: 0P and 18B. BP4_ModerateBP6_Very_StrongBA1
The NM_003289.4(TPM2):c.*8G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0855 in 1,552,166 control chromosomes in the GnomAD database, including 6,178 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_003289.4 3_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -18 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
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TPM2 | NM_003289.4 | c.*8G>A | 3_prime_UTR_variant | Exon 9 of 9 | ENST00000645482.3 | NP_003280.2 | ||
TPM2 | NM_001301227.2 | c.*8G>A | 3_prime_UTR_variant | Exon 9 of 9 | NP_001288156.1 | |||
TPM2 | NM_001301226.2 | c.773-988G>A | intron_variant | Intron 8 of 8 | NP_001288155.1 | |||
TPM2 | NM_213674.1 | c.773-988G>A | intron_variant | Intron 8 of 8 | NP_998839.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0632 AC: 9609AN: 152014Hom.: 372 Cov.: 32
GnomAD3 exomes AF: 0.0760 AC: 12096AN: 159072Hom.: 511 AF XY: 0.0785 AC XY: 6571AN XY: 83690
GnomAD4 exome AF: 0.0879 AC: 123047AN: 1400034Hom.: 5806 Cov.: 33 AF XY: 0.0885 AC XY: 61092AN XY: 690674
GnomAD4 genome AF: 0.0632 AC: 9614AN: 152132Hom.: 372 Cov.: 32 AF XY: 0.0608 AC XY: 4525AN XY: 74402
ClinVar
Submissions by phenotype
not specified Benign:8
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
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*8G>A in exon 9A of TPM2: This variant is not expected to have clinical signific ance because it has been identified in 8.9% (757/8480) of European American chro mosomes from a broad population by the NHLBI Exome Sequencing Project (http://ev s.gs.washington.edu/EVS; dbSNP rs56249943). -
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not provided Benign:1Other:1
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Arthrogryposis, distal, type 1A 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 23 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. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at