chr2-240573147-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_018226.6(RNPEPL1):c.707G>A(p.Arg236Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000193 in 1,610,242 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R236W) has been classified as Uncertain significance.
Frequency
Consequence
NM_018226.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RNPEPL1 | NM_018226.6 | c.707G>A | p.Arg236Gln | missense_variant | 3/11 | ENST00000270357.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RNPEPL1 | ENST00000270357.10 | c.707G>A | p.Arg236Gln | missense_variant | 3/11 | 1 | NM_018226.6 | P1 | |
RNPEPL1 | ENST00000451363.5 | c.-56-1368G>A | intron_variant | 4 | |||||
RNPEPL1 | ENST00000486058.5 | n.433G>A | non_coding_transcript_exon_variant | 3/9 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000460 AC: 7AN: 152142Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.00000412 AC: 1AN: 242672Hom.: 0 AF XY: 0.00000760 AC XY: 1AN XY: 131656
GnomAD4 exome AF: 0.0000165 AC: 24AN: 1457982Hom.: 0 Cov.: 33 AF XY: 0.0000138 AC XY: 10AN XY: 724980
GnomAD4 genome ? AF: 0.0000460 AC: 7AN: 152260Hom.: 0 Cov.: 34 AF XY: 0.0000672 AC XY: 5AN XY: 74448
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 22, 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