chr18-8784055-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001395333.1(MTCL1):c.2023C>T(p.Arg675Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000031 in 1,613,308 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001395333.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MTCL1 | NM_001395333.1 | c.2023C>T | p.Arg675Trp | missense_variant | 5/15 | ENST00000695636.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MTCL1 | ENST00000695636.1 | c.2023C>T | p.Arg675Trp | missense_variant | 5/15 | NM_001395333.1 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.000105 AC: 16AN: 152166Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000404 AC: 10AN: 247656Hom.: 0 AF XY: 0.0000296 AC XY: 4AN XY: 135016
GnomAD4 exome AF: 0.0000233 AC: 34AN: 1461142Hom.: 0 Cov.: 92 AF XY: 0.0000234 AC XY: 17AN XY: 726850
GnomAD4 genome ? AF: 0.000105 AC: 16AN: 152166Hom.: 0 Cov.: 33 AF XY: 0.0000942 AC XY: 7AN XY: 74330
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 12, 2021 | The c.943C>T (p.R315W) alteration is located in exon 6 (coding exon 4) of the MTCL1 gene. This alteration results from a C to T substitution at nucleotide position 943, causing the arginine (R) at amino acid position 315 to be replaced by a tryptophan (W). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at