1-201996239-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 3P and 1B. PM2PP3BP4
The NM_020216.4(RNPEP):āc.830T>Cā(p.Leu277Pro) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000657 in 1,612,712 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. L277F) has been classified as Uncertain significance.
Frequency
Consequence
NM_020216.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RNPEP | NM_020216.4 | c.830T>C | p.Leu277Pro | missense_variant | 4/11 | ENST00000295640.9 | |
RNPEP | NM_001319182.2 | c.437T>C | p.Leu146Pro | missense_variant | 4/11 | ||
RNPEP | NM_001319183.2 | c.-187T>C | 5_prime_UTR_variant | 3/10 | |||
RNPEP | NM_001319184.2 | c.-41T>C | 5_prime_UTR_variant | 3/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RNPEP | ENST00000295640.9 | c.830T>C | p.Leu277Pro | missense_variant | 4/11 | 1 | NM_020216.4 | P1 | |
ELF3-AS1 | ENST00000419190.2 | n.4753A>G | non_coding_transcript_exon_variant | 2/2 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.000316 AC: 48AN: 152104Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000795 AC: 20AN: 251470Hom.: 0 AF XY: 0.0000441 AC XY: 6AN XY: 135908
GnomAD4 exome AF: 0.0000397 AC: 58AN: 1460490Hom.: 0 Cov.: 29 AF XY: 0.0000248 AC XY: 18AN XY: 726676
GnomAD4 genome ? AF: 0.000315 AC: 48AN: 152222Hom.: 0 Cov.: 32 AF XY: 0.000349 AC XY: 26AN XY: 74406
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 04, 2024 | The c.830T>C (p.L277P) alteration is located in exon 4 (coding exon 4) of the RNPEP gene. This alteration results from a T to C substitution at nucleotide position 830, causing the leucine (L) at amino acid position 277 to be replaced by a proline (P). 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