6-112349792-C-A
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_001013734.3(RFPL4B):c.84C>A(p.His28Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000434 in 1,613,928 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_001013734.3 missense
Scores
Clinical Significance
Conservation
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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 |
---|---|---|---|---|---|---|---|---|---|---|
RFPL4B | ENST00000441065.3 | c.84C>A | p.His28Gln | missense_variant | Exon 3 of 3 | 2 | NM_001013734.3 | ENSP00000423391.1 | ||
ENSG00000281613 | ENST00000587816.2 | c.84C>A | p.His28Gln | missense_variant | Exon 5 of 5 | 5 | ENSP00000487146.1 | |||
ENSG00000281613 | ENST00000585611.5 | c.84C>A | p.His28Gln | missense_variant | Exon 5 of 5 | 5 | ENSP00000486440.1 | |||
ENSG00000281613 | ENST00000590673.5 | c.84C>A | p.His28Gln | missense_variant | Exon 4 of 4 | 5 | ENSP00000486934.1 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152138Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1461790Hom.: 0 Cov.: 31 AF XY: 0.00000413 AC XY: 3AN XY: 727206
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152138Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74308
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.84C>A (p.H28Q) alteration is located in exon 3 (coding exon 1) of the RFPL4B gene. This alteration results from a C to A substitution at nucleotide position 84, causing the histidine (H) at amino acid position 28 to be replaced by a glutamine (Q). 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