1-201982707-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_020216.4(RNPEP):c.41G>A(p.Arg14Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000458 in 1,398,370 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_020216.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RNPEP | NM_020216.4 | c.41G>A | p.Arg14Gln | missense_variant | 1/11 | ENST00000295640.9 | |
RNPEP | NM_001319183.2 | c.-827G>A | 5_prime_UTR_variant | 1/10 | |||
RNPEP | NM_001319184.2 | c.-681G>A | 5_prime_UTR_variant | 1/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RNPEP | ENST00000295640.9 | c.41G>A | p.Arg14Gln | missense_variant | 1/11 | 1 | NM_020216.4 | P1 | |
RNPEP | ENST00000367286.7 | c.41G>A | p.Arg14Gln | missense_variant | 1/10 | 5 | |||
RNPEP | ENST00000481780.5 | n.66+270G>A | intron_variant, non_coding_transcript_variant | 5 | |||||
RNPEP | ENST00000487116.5 | upstream_gene_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.000112 AC: 17AN: 151426Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000192 AC: 1AN: 52128Hom.: 0 AF XY: 0.0000333 AC XY: 1AN XY: 30028
GnomAD4 exome AF: 0.0000377 AC: 47AN: 1246836Hom.: 0 Cov.: 29 AF XY: 0.0000360 AC XY: 22AN XY: 611792
GnomAD4 genome ? AF: 0.000112 AC: 17AN: 151534Hom.: 0 Cov.: 32 AF XY: 0.000135 AC XY: 10AN XY: 74090
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 18, 2023 | The c.41G>A (p.R14Q) alteration is located in exon 1 (coding exon 1) of the RNPEP gene. This alteration results from a G to A substitution at nucleotide position 41, causing the arginine (R) at amino acid position 14 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