rs533504444
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 1P and 8B. PP3BP6_Very_Strong
The NM_003283.6(TNNT1):c.46G>C(p.Glu16Gln) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000102 in 1,610,072 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 2/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Likely benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. E16K) has been classified as Uncertain significance.
Frequency
Consequence
NM_003283.6 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TNNT1 | NM_003283.6 | c.46G>C | p.Glu16Gln | missense_variant, splice_region_variant | 3/14 | ENST00000588981.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TNNT1 | ENST00000588981.6 | c.46G>C | p.Glu16Gln | missense_variant, splice_region_variant | 3/14 | 1 | NM_003283.6 |
Frequencies
GnomAD3 genomes ? AF: 0.0000394 AC: 6AN: 152194Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000260 AC: 63AN: 241948Hom.: 1 AF XY: 0.000322 AC XY: 42AN XY: 130630
GnomAD4 exome AF: 0.000109 AC: 159AN: 1457760Hom.: 0 Cov.: 32 AF XY: 0.000152 AC XY: 110AN XY: 724670
GnomAD4 genome ? AF: 0.0000394 AC: 6AN: 152312Hom.: 1 Cov.: 32 AF XY: 0.0000671 AC XY: 5AN XY: 74476
ClinVar
Submissions by phenotype
Nemaline myopathy 5 Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Al Jalila Children’s Genomics Center, Al Jalila Childrens Speciality Hospital | Mar 22, 2020 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Sep 01, 2023 | - - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jan 29, 2018 | 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. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at