chr2-178774997-C-T
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6_Very_StrongBP7
The NM_001267550.2(TTN):c.6714G>A(p.Thr2238=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000242 in 1,613,770 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. T2238T) has been classified as Likely benign.
Frequency
Consequence
NM_001267550.2 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TTN | NM_001267550.2 | c.6714G>A | p.Thr2238= | synonymous_variant | 29/363 | ENST00000589042.5 | |
TTN | NM_133379.5 | c.6714G>A | p.Thr2238= | synonymous_variant | 29/46 | ENST00000360870.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TTN | ENST00000589042.5 | c.6714G>A | p.Thr2238= | synonymous_variant | 29/363 | 5 | NM_001267550.2 | P1 | |
TTN | ENST00000360870.10 | c.6714G>A | p.Thr2238= | synonymous_variant | 29/46 | 5 | NM_133379.5 | ||
TTN-AS1 | ENST00000659121.1 | n.2424C>T | non_coding_transcript_exon_variant | 12/13 |
Frequencies
GnomAD3 genomes AF: 0.000105 AC: 16AN: 152140Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.0000319 AC: 8AN: 251094Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135712
GnomAD4 exome AF: 0.0000157 AC: 23AN: 1461630Hom.: 0 Cov.: 33 AF XY: 0.0000151 AC XY: 11AN XY: 727108
GnomAD4 genome AF: 0.000105 AC: 16AN: 152140Hom.: 1 Cov.: 32 AF XY: 0.0000673 AC XY: 5AN XY: 74320
ClinVar
Submissions by phenotype
Autosomal recessive limb-girdle muscular dystrophy type 2J;C1858763:Dilated cardiomyopathy 1G Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 05, 2023 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 26, 2018 | - - |
Cardiovascular phenotype Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | May 21, 2015 | 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