19-2477576-C-T
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_015675.4(GADD45B):c.458C>T(p.Pro153Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000657 in 152,168 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_015675.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GADD45B | ENST00000215631.9 | c.458C>T | p.Pro153Leu | missense_variant | Exon 4 of 4 | 1 | NM_015675.4 | ENSP00000215631.3 | ||
GADD45B | ENST00000585359.1 | n.*273C>T | non_coding_transcript_exon_variant | Exon 4 of 4 | 3 | ENSP00000466414.1 | ||||
GADD45B | ENST00000592937.1 | n.1324C>T | non_coding_transcript_exon_variant | Exon 2 of 2 | 2 | |||||
GADD45B | ENST00000585359.1 | n.*273C>T | 3_prime_UTR_variant | Exon 4 of 4 | 3 | ENSP00000466414.1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152168Hom.: 0 Cov.: 32
GnomAD4 exome Cov.: 30
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152168Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74340
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.458C>T (p.P153L) alteration is located in exon 4 (coding exon 4) of the GADD45B gene. This alteration results from a C to T substitution at nucleotide position 458, causing the proline (P) at amino acid position 153 to be replaced by a leucine (L). 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