18-8783978-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001395333.1(MTCL1):c.1946G>A(p.Arg649Gln) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000347 in 1,613,674 control chromosomes in the GnomAD database, including 1 homozygotes. 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. R649W) 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.1946G>A | p.Arg649Gln | missense_variant | 5/15 | ENST00000695636.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MTCL1 | ENST00000695636.1 | c.1946G>A | p.Arg649Gln | missense_variant | 5/15 | NM_001395333.1 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000460 AC: 7AN: 152184Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000359 AC: 9AN: 250578Hom.: 1 AF XY: 0.0000516 AC XY: 7AN XY: 135776
GnomAD4 exome AF: 0.0000335 AC: 49AN: 1461490Hom.: 1 Cov.: 91 AF XY: 0.0000371 AC XY: 27AN XY: 727052
GnomAD4 genome ? AF: 0.0000460 AC: 7AN: 152184Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74332
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 27, 2022 | The c.866G>A (p.R289Q) alteration is located in exon 6 (coding exon 4) of the MTCL1 gene. This alteration results from a G to A substitution at nucleotide position 866, causing the arginine (R) at amino acid position 289 to be replaced by a glutamine (Q). 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