chr2-178756224-C-T
Variant summary
Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001267550.2(TTN):c.11252G>A(p.Gly3751Asp) variant causes a missense, splice region change. The variant allele was found at a frequency of 0.9 in 1,594,874 control chromosomes in the GnomAD database, including 650,799 homozygotes. In-silico tool predicts a benign outcome for this variant. 11/17 in silico tools predict a benign outcome for this variant. 2/2 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G3751E) has been classified as Uncertain significance.
Frequency
Consequence
NM_001267550.2 missense, splice_region
Scores
Clinical Significance
Conservation
Publications
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ACMG classification
Our verdict: Benign. The variant received -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
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TTN | NM_001267550.2 | c.11252G>A | p.Gly3751Asp | missense_variant, splice_region_variant | Exon 46 of 363 | ENST00000589042.5 | NP_001254479.2 | |
TTN | NM_133379.5 | c.10303+2760G>A | intron_variant | Intron 44 of 45 | ENST00000360870.10 | NP_596870.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TTN | ENST00000589042.5 | c.11252G>A | p.Gly3751Asp | missense_variant, splice_region_variant | Exon 46 of 363 | 5 | NM_001267550.2 | ENSP00000467141.1 | ||
TTN | ENST00000360870.10 | c.10303+2760G>A | intron_variant | Intron 44 of 45 | 5 | NM_133379.5 | ENSP00000354117.4 |
Frequencies
GnomAD3 genomes AF: 0.870 AC: 132390AN: 152096Hom.: 58094 Cov.: 33 show subpopulations
GnomAD2 exomes AF: 0.838 AC: 203686AN: 242962 AF XY: 0.850 show subpopulations
GnomAD4 exome AF: 0.903 AC: 1303069AN: 1442660Hom.: 592684 Cov.: 30 AF XY: 0.902 AC XY: 644760AN XY: 714838 show subpopulations
Age Distribution
GnomAD4 genome AF: 0.870 AC: 132452AN: 152214Hom.: 58115 Cov.: 33 AF XY: 0.865 AC XY: 64327AN XY: 74408 show subpopulations
Age Distribution
ClinVar
Submissions by phenotype
not specified Benign:7
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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not provided Benign:2
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Autosomal recessive limb-girdle muscular dystrophy type 2J;C1858763:Dilated cardiomyopathy 1G Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at