rs397517816
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_133379.5(TTN):c.15338C>T(p.Ala5113Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000217 in 1,613,056 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/14 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_133379.5 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_133379.5 | c.15338C>T | p.Ala5113Val | missense_variant | 46/46 | ENST00000360870.10 | |
TTN | NM_001267550.2 | c.11312-5141C>T | intron_variant | ENST00000589042.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TTN | ENST00000360870.10 | c.15338C>T | p.Ala5113Val | missense_variant | 46/46 | 5 | NM_133379.5 | ||
TTN | ENST00000589042.5 | c.11312-5141C>T | intron_variant | 5 | NM_001267550.2 | P1 | |||
TTN-AS1 | ENST00000659121.1 | n.1223+4092G>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.0000132 AC: 2AN: 151872Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000640 AC: 16AN: 250124Hom.: 0 AF XY: 0.0000961 AC XY: 13AN XY: 135264
GnomAD4 exome AF: 0.0000226 AC: 33AN: 1461184Hom.: 0 Cov.: 34 AF XY: 0.0000371 AC XY: 27AN XY: 726882
GnomAD4 genome ? AF: 0.0000132 AC: 2AN: 151872Hom.: 0 Cov.: 32 AF XY: 0.0000270 AC XY: 2AN XY: 74170
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Jul 26, 2013 | The Ala5113Val variant in TTN has been identified by our laboratory in 1 individ ual with HCM, who carried a pathogenic variant in another gene (LMM unpublished data). Computational analyses (biochemical amino acid properties, conservation, AlignGVGD, PolyPhen2, and SIFT) are limited or unavailable for this variant. Add itional information is needed to fully assess the clinical significance of this variant. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at