chr18-8783977-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001395333.1(MTCL1):c.1945C>T(p.Arg649Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000508 in 1,613,660 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R649Q) has been classified 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 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MTCL1 | NM_001395333.1 | c.1945C>T | p.Arg649Trp | missense_variant | 5/15 | ENST00000695636.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MTCL1 | ENST00000695636.1 | c.1945C>T | p.Arg649Trp | missense_variant | 5/15 | NM_001395333.1 | A2 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152166Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000878 AC: 22AN: 250644Hom.: 0 AF XY: 0.000103 AC XY: 14AN XY: 135792
GnomAD4 exome AF: 0.0000513 AC: 75AN: 1461494Hom.: 0 Cov.: 91 AF XY: 0.0000605 AC XY: 44AN XY: 727052
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152166Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74326
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 04, 2022 | The c.865C>T (p.R289W) 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 865, causing the arginine (R) at amino acid position 289 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