chr9-4844656-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_005772.5(RCL1):c.842G>A(p.Arg281Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000353 in 1,613,522 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_005772.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RCL1 | NM_005772.5 | c.842G>A | p.Arg281Gln | missense_variant | 7/9 | ENST00000381750.9 | |
RCL1 | NM_001286699.2 | c.368G>A | p.Arg123Gln | missense_variant | 5/7 | ||
RCL1 | NM_001286700.2 | c.368G>A | p.Arg123Gln | missense_variant | 6/8 | ||
RCL1 | NM_001286701.2 | c.284G>A | p.Arg95Gln | missense_variant | 3/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RCL1 | ENST00000381750.9 | c.842G>A | p.Arg281Gln | missense_variant | 7/9 | 1 | NM_005772.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152204Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000359 AC: 9AN: 250520Hom.: 0 AF XY: 0.0000517 AC XY: 7AN XY: 135384
GnomAD4 exome AF: 0.0000376 AC: 55AN: 1461200Hom.: 0 Cov.: 33 AF XY: 0.0000523 AC XY: 38AN XY: 726900
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152322Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74474
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 22, 2023 | The c.842G>A (p.R281Q) alteration is located in exon 7 (coding exon 7) of the RCL1 gene. This alteration results from a G to A substitution at nucleotide position 842, causing the arginine (R) at amino acid position 281 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