chr2-178594523-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 1P and 5B. PP2BP4_StrongBP6
The NM_001267550.2(TTN):c.57971G>A(p.Arg19324Gln) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000236 in 1,613,298 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R19324W) has been classified as Uncertain significance.
Frequency
Consequence
NM_001267550.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TTN | NM_001267550.2 | c.57971G>A | p.Arg19324Gln | missense_variant | 296/363 | ENST00000589042.5 | |
TTN-AS1 | NR_038272.1 | n.3365-3073C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TTN | ENST00000589042.5 | c.57971G>A | p.Arg19324Gln | missense_variant | 296/363 | 5 | NM_001267550.2 | P1 | |
TTN-AS1 | ENST00000659121.1 | n.417-3073C>T | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 151994Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000724 AC: 18AN: 248630Hom.: 0 AF XY: 0.0000667 AC XY: 9AN XY: 134872
GnomAD4 exome AF: 0.0000205 AC: 30AN: 1461186Hom.: 0 Cov.: 33 AF XY: 0.0000151 AC XY: 11AN XY: 726874
GnomAD4 genome AF: 0.0000526 AC: 8AN: 152112Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74356
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:1
Uncertain significance, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | Dec 07, 2020 | - - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 16, 2019 | This variant is associated with the following publications: (PMID: 31983221) - |
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Jun 27, 2014 | The Arg16756Gln variant in TTN has not been previously reported in individuals w ith cardiomyopathy, but has been identified in 1/200 Southern Han Chinese chromo somes by the 1000 Genomes Project (dbSNP rs186809500). Computational prediction tools and conservation analysis suggest that this variant may impact the protein , though this information is not predictive enough to determine pathogenicity. I n summary, the clinical significance of the Arg16756Gln variant is uncertain. - |
Cardiovascular phenotype Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 24, 2019 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at