22-29438958-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_021026.2(RFPL1):c.167G>A(p.Gly56Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000118 in 1,613,852 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_021026.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RFPL1 | NM_021026.2 | c.167G>A | p.Gly56Glu | missense_variant | 1/2 | NP_066306.2 | ||
RFPL1 | NM_001393612.1 | c.80G>A | p.Gly27Glu | missense_variant | 9/10 | NP_001380541.1 | ||
RFPL1S | NR_002727.2 | n.3172C>T | non_coding_transcript_exon_variant | 1/1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RFPL1 | ENST00000354373.2 | c.167G>A | p.Gly56Glu | missense_variant | 1/2 | 1 | ENSP00000346342.2 | |||
RFPL1S | ENST00000248980.9 | n.507C>T | non_coding_transcript_exon_variant | 3/3 | 1 | |||||
RFPL1S | ENST00000461286.4 | n.3479C>T | non_coding_transcript_exon_variant | 3/3 | 4 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152170Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251224Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135770
GnomAD4 exome AF: 0.0000109 AC: 16AN: 1461682Hom.: 0 Cov.: 33 AF XY: 0.00000825 AC XY: 6AN XY: 727150
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152170Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74348
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 23, 2023 | The c.167G>A (p.G56E) alteration is located in exon 1 (coding exon 1) of the RFPL1 gene. This alteration results from a G to A substitution at nucleotide position 167, causing the glycine (G) at amino acid position 56 to be replaced by a glutamic acid (E). 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