chr20-45314036-T-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BA1
The NM_014276.4(RBPJL):c.759T>C(p.Ala253=) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0514 in 1,611,092 control chromosomes in the GnomAD database, including 5,200 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (no stars).
Frequency
Consequence
NM_014276.4 splice_region, synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RBPJL | NM_014276.4 | c.759T>C | p.Ala253= | splice_region_variant, synonymous_variant | 8/12 | ENST00000343694.8 | |
RBPJL | NM_001281449.2 | c.759T>C | p.Ala253= | splice_region_variant, synonymous_variant | 8/12 | ||
RBPJL | NM_001281448.2 | c.759T>C | p.Ala253= | splice_region_variant, synonymous_variant | 8/12 | ||
RBPJL | XM_011528522.3 | c.759T>C | p.Ala253= | splice_region_variant, synonymous_variant | 8/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RBPJL | ENST00000343694.8 | c.759T>C | p.Ala253= | splice_region_variant, synonymous_variant | 8/12 | 1 | NM_014276.4 | A1 | |
RBPJL | ENST00000372743.5 | c.759T>C | p.Ala253= | splice_region_variant, synonymous_variant | 8/12 | 1 | P4 | ||
RBPJL | ENST00000372741.7 | c.759T>C | p.Ala253= | splice_region_variant, synonymous_variant | 8/12 | 1 | |||
RBPJL | ENST00000464504.2 | c.3T>C | p.Ter1= | coding_sequence_variant | 1/5 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0457 AC: 6955AN: 152190Hom.: 475 Cov.: 33
GnomAD3 exomes AF: 0.0912 AC: 22898AN: 251146Hom.: 2342 AF XY: 0.0905 AC XY: 12279AN XY: 135736
GnomAD4 exome AF: 0.0520 AC: 75851AN: 1458784Hom.: 4724 Cov.: 31 AF XY: 0.0546 AC XY: 39653AN XY: 725862
GnomAD4 genome ? AF: 0.0456 AC: 6950AN: 152308Hom.: 476 Cov.: 33 AF XY: 0.0507 AC XY: 3774AN XY: 74482
ClinVar
Submissions by phenotype
Type 2 diabetes mellitus Benign:1
Benign, no assertion criteria provided | case-control | Diabetes Molecular Genetics Section, Phoenix Epidemiology and Clinical Research Branch, National Institutes of Health | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at