chr2-240568795-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_018226.6(RNPEPL1):c.209C>A(p.Pro70His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000554 in 1,082,146 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 8/12 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_018226.6 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 | UniProt |
---|---|---|---|---|---|---|---|
RNPEPL1 | NM_018226.6 | c.209C>A | p.Pro70His | missense_variant | 1/11 | ENST00000270357.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RNPEPL1 | ENST00000270357.10 | c.209C>A | p.Pro70His | missense_variant | 1/11 | 1 | NM_018226.6 | P1 | |
ANKMY1 | ENST00000418708.3 | c.-122+241G>T | intron_variant | 3 | |||||
RNPEPL1 | ENST00000451363.5 | c.-57+2854C>A | intron_variant | 4 | |||||
ANKMY1 | ENST00000418505.3 | n.174+241G>T | intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000272 AC: 4AN: 147104Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000214 AC: 2AN: 935042Hom.: 0 Cov.: 31 AF XY: 0.00000225 AC XY: 1AN XY: 444026
GnomAD4 genome ? AF: 0.0000272 AC: 4AN: 147104Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 71592
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 20, 2021 | The c.209C>A (p.P70H) alteration is located in exon 1 (coding exon 1) of the RNPEPL1 gene. This alteration results from a C to A substitution at nucleotide position 209, causing the proline (P) at amino acid position 70 to be replaced by a histidine (H). 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