19-55157624-G-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_000363.5(TNNI3):c.-35C>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0145 in 1,613,762 control chromosomes in the GnomAD database, including 2,191 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_000363.5 5_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TNNI3 | ENST00000344887.10 | c.-35C>A | 5_prime_UTR_variant | Exon 1 of 8 | 1 | NM_000363.5 | ENSP00000341838.5 | |||
ENSG00000267110 | ENST00000587871.1 | n.*69C>A | non_coding_transcript_exon_variant | Exon 5 of 9 | 5 | ENSP00000473050.1 | ||||
ENSG00000267110 | ENST00000587871.1 | n.*69C>A | 3_prime_UTR_variant | Exon 5 of 9 | 5 | ENSP00000473050.1 |
Frequencies
GnomAD3 genomes AF: 0.0684 AC: 10397AN: 152084Hom.: 1126 Cov.: 32
GnomAD3 exomes AF: 0.0196 AC: 4881AN: 248884Hom.: 471 AF XY: 0.0156 AC XY: 2105AN XY: 135142
GnomAD4 exome AF: 0.00892 AC: 13042AN: 1461560Hom.: 1058 Cov.: 32 AF XY: 0.00798 AC XY: 5800AN XY: 727076
GnomAD4 genome AF: 0.0686 AC: 10436AN: 152202Hom.: 1133 Cov.: 32 AF XY: 0.0660 AC XY: 4916AN XY: 74434
ClinVar
Submissions by phenotype
not specified Benign:2
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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Cardiomyopathy, familial restrictive, 1 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. -
Familial Hypertrophic Cardiomyopathy with Wolff-Parkinson-White Syndrome Benign:1
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Hypertrophic cardiomyopathy 7 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. -
Primary ciliary dyskinesia Benign:1
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Dilated Cardiomyopathy, Recessive Benign:1
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not provided Benign:1
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Familial restrictive cardiomyopathy Benign:1
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Dilated cardiomyopathy 2A 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. -
Hypertrophic cardiomyopathy Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at