19-55141915-G-A
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4_StrongBP6
The NM_003283.6(TNNT1):c.134C>T(p.Pro45Leu) variant causes a missense change. The variant allele was found at a frequency of 0.0000917 in 1,614,020 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. P45P) has been classified as Likely benign.
Frequency
Consequence
NM_003283.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TNNT1 | NM_003283.6 | c.134C>T | p.Pro45Leu | missense_variant | 7/14 | ENST00000588981.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TNNT1 | ENST00000588981.6 | c.134C>T | p.Pro45Leu | missense_variant | 7/14 | 1 | NM_003283.6 |
Frequencies
GnomAD3 genomes AF: 0.000118 AC: 18AN: 152128Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000350 AC: 88AN: 251376Hom.: 0 AF XY: 0.000331 AC XY: 45AN XY: 135858
GnomAD4 exome AF: 0.0000889 AC: 130AN: 1461774Hom.: 0 Cov.: 31 AF XY: 0.000102 AC XY: 74AN XY: 727194
GnomAD4 genome AF: 0.000118 AC: 18AN: 152246Hom.: 0 Cov.: 32 AF XY: 0.000134 AC XY: 10AN XY: 74432
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Jun 01, 2016 | - - |
Nemaline myopathy 5 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 30, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at