chr1-67687727-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PP3_ModerateBS2
The NM_001924.4(GADD45A):c.451C>T(p.Arg151Cys) variant causes a missense change. The variant allele was found at a frequency of 0.00000434 in 1,613,040 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_001924.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GADD45A | NM_001924.4 | c.451C>T | p.Arg151Cys | missense_variant | Exon 4 of 4 | ENST00000370986.9 | NP_001915.1 | |
GADD45A | NM_001199741.2 | c.349C>T | p.Arg117Cys | missense_variant | Exon 3 of 3 | NP_001186670.1 | ||
GADD45A | NM_001199742.2 | c.*30C>T | 3_prime_UTR_variant | Exon 3 of 3 | NP_001186671.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152214Hom.: 0 Cov.: 33
GnomAD4 exome AF: 0.00000411 AC: 6AN: 1460826Hom.: 0 Cov.: 29 AF XY: 0.00000275 AC XY: 2AN XY: 726758
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152214Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74362
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.451C>T (p.R151C) alteration is located in exon 4 (coding exon 4) of the GADD45A gene. This alteration results from a C to T substitution at nucleotide position 451, causing the arginine (R) at amino acid position 151 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