3-8881404-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_020165.4(RAD18):c.1441G>A(p.Ala481Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000676 in 1,613,172 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_020165.4 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RAD18 | NM_020165.4 | c.1441G>A | p.Ala481Thr | missense_variant | 13/13 | ENST00000264926.7 | |
RAD18 | XM_017006873.2 | c.1183G>A | p.Ala395Thr | missense_variant | 11/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RAD18 | ENST00000264926.7 | c.1441G>A | p.Ala481Thr | missense_variant | 13/13 | 1 | NM_020165.4 | P1 | |
RAD18 | ENST00000427329.5 | c.294+8985G>A | intron_variant | 3 | |||||
RAD18 | ENST00000415439.5 | c.*431G>A | 3_prime_UTR_variant, NMD_transcript_variant | 12/12 | 5 | ||||
RAD18 | ENST00000473069.1 | downstream_gene_variant | 4 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152186Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000438 AC: 11AN: 251308Hom.: 0 AF XY: 0.0000736 AC XY: 10AN XY: 135840
GnomAD4 exome AF: 0.0000719 AC: 105AN: 1460986Hom.: 0 Cov.: 30 AF XY: 0.0000674 AC XY: 49AN XY: 726838
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152186Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74358
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 12, 2023 | The c.1441G>A (p.A481T) alteration is located in exon 13 (coding exon 13) of the RAD18 gene. This alteration results from a G to A substitution at nucleotide position 1441, causing the alanine (A) at amino acid position 481 to be replaced by a threonine (T). 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