22-41230150-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_031488.5(L3MBTL2):c.2017C>T(p.Arg673Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000725 in 1,241,690 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/23 in silico tools predict a benign outcome for this variant. 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. R673H) has been classified as Uncertain significance.
Frequency
Consequence
NM_031488.5 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
L3MBTL2 | NM_031488.5 | c.2017C>T | p.Arg673Cys | missense_variant | Exon 17 of 17 | ENST00000216237.10 | NP_113676.2 | |
CHADL | NM_138481.2 | c.2263-420G>A | intron_variant | Intron 5 of 5 | ENST00000216241.14 | NP_612490.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
L3MBTL2 | ENST00000216237.10 | c.2017C>T | p.Arg673Cys | missense_variant | Exon 17 of 17 | 1 | NM_031488.5 | ENSP00000216237.5 | ||
CHADL | ENST00000216241.14 | c.2263-420G>A | intron_variant | Intron 5 of 5 | 1 | NM_138481.2 | ENSP00000216241.9 |
Frequencies
GnomAD3 genomes AF: 0.0000292 AC: 4AN: 136864Hom.: 0 Cov.: 29
GnomAD3 exomes AF: 0.00000798 AC: 2AN: 250666Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135582
GnomAD4 exome AF: 0.00000453 AC: 5AN: 1104826Hom.: 0 Cov.: 31 AF XY: 0.00000542 AC XY: 3AN XY: 553574
GnomAD4 genome AF: 0.0000292 AC: 4AN: 136864Hom.: 0 Cov.: 29 AF XY: 0.0000305 AC XY: 2AN XY: 65588
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.2017C>T (p.R673C) alteration is located in exon 17 (coding exon 17) of the L3MBTL2 gene. This alteration results from a C to T substitution at nucleotide position 2017, causing the arginine (R) at amino acid position 673 to be replaced by a cysteine (C). 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