22-41229564-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.1913C>T(p.Thr638Met) variant causes a missense change. The variant allele was found at a frequency of 0.0000453 in 1,612,638 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar 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.1913C>T | p.Thr638Met | missense_variant | Exon 16 of 17 | ENST00000216237.10 | NP_113676.2 | |
CHADL | NM_138481.2 | c.*140G>A | 3_prime_UTR_variant | Exon 6 of 6 | ENST00000216241.14 | NP_612490.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
L3MBTL2 | ENST00000216237.10 | c.1913C>T | p.Thr638Met | missense_variant | Exon 16 of 17 | 1 | NM_031488.5 | ENSP00000216237.5 | ||
CHADL | ENST00000216241 | c.*140G>A | 3_prime_UTR_variant | Exon 6 of 6 | 1 | NM_138481.2 | ENSP00000216241.9 |
Frequencies
GnomAD3 genomes AF: 0.0000723 AC: 11AN: 152210Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000239 AC: 6AN: 251080Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135754
GnomAD4 exome AF: 0.0000425 AC: 62AN: 1460428Hom.: 0 Cov.: 31 AF XY: 0.0000441 AC XY: 32AN XY: 726196
GnomAD4 genome AF: 0.0000723 AC: 11AN: 152210Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74364
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1913C>T (p.T638M) alteration is located in exon 16 (coding exon 16) of the L3MBTL2 gene. This alteration results from a C to T substitution at nucleotide position 1913, causing the threonine (T) at amino acid position 638 to be replaced by a methionine (M). 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