chr8-94372355-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_ModerateBP6_Moderate
The NM_012415.3(RAD54B):c.2548G>A(p.Asp850Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000236 in 1,613,186 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_012415.3 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 |
---|---|---|---|---|---|---|---|
RAD54B | NM_012415.3 | c.2548G>A | p.Asp850Asn | missense_variant | 15/15 | ENST00000336148.10 | |
RAD54B | NM_001205263.2 | c.1996G>A | p.Asp666Asn | missense_variant | 13/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RAD54B | ENST00000336148.10 | c.2548G>A | p.Asp850Asn | missense_variant | 15/15 | 1 | NM_012415.3 | P1 | |
RAD54B | ENST00000519348.1 | n.112G>A | non_coding_transcript_exon_variant | 2/2 | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000394 AC: 6AN: 152168Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000519 AC: 13AN: 250608Hom.: 0 AF XY: 0.0000590 AC XY: 8AN XY: 135540
GnomAD4 exome AF: 0.0000219 AC: 32AN: 1461018Hom.: 0 Cov.: 31 AF XY: 0.0000138 AC XY: 10AN XY: 726822
GnomAD4 genome ? AF: 0.0000394 AC: 6AN: 152168Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74326
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 21, 2021 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at