20-45314116-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_014276.4(RBPJL):c.839C>T(p.Thr280Met) variant causes a missense change. The variant allele was found at a frequency of 0.000428 in 1,614,030 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as risk factor (no stars).
Frequency
Consequence
NM_014276.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RBPJL | NM_014276.4 | c.839C>T | p.Thr280Met | missense_variant | Exon 8 of 12 | ENST00000343694.8 | NP_055091.2 | |
RBPJL | NM_001281449.2 | c.839C>T | p.Thr280Met | missense_variant | Exon 8 of 12 | NP_001268378.1 | ||
RBPJL | NM_001281448.2 | c.839C>T | p.Thr280Met | missense_variant | Exon 8 of 12 | NP_001268377.1 | ||
RBPJL | XM_011528522.3 | c.839C>T | p.Thr280Met | missense_variant | Exon 8 of 12 | XP_011526824.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RBPJL | ENST00000343694.8 | c.839C>T | p.Thr280Met | missense_variant | Exon 8 of 12 | 1 | NM_014276.4 | ENSP00000341243.3 | ||
RBPJL | ENST00000372743.5 | c.839C>T | p.Thr280Met | missense_variant | Exon 8 of 12 | 1 | ENSP00000361828.1 | |||
RBPJL | ENST00000372741.7 | c.839C>T | p.Thr280Met | missense_variant | Exon 8 of 12 | 1 | ENSP00000361826.3 | |||
RBPJL | ENST00000464504.2 | c.80C>T | p.Thr27Met | missense_variant | Exon 1 of 5 | 3 | ENSP00000483978.1 |
Frequencies
GnomAD3 genomes AF: 0.000466 AC: 71AN: 152232Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00166 AC: 418AN: 251118Hom.: 0 AF XY: 0.00124 AC XY: 168AN XY: 135810
GnomAD4 exome AF: 0.000421 AC: 616AN: 1461680Hom.: 1 Cov.: 31 AF XY: 0.000358 AC XY: 260AN XY: 727176
GnomAD4 genome AF: 0.000486 AC: 74AN: 152350Hom.: 0 Cov.: 33 AF XY: 0.000470 AC XY: 35AN XY: 74498
ClinVar
Submissions by phenotype
Type 2 diabetes mellitus Other:1
The variant allele associates with increased risk of T2D. In in-vtro studies the variant allele reduces protein expression and also effects tranactivation capability -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at