chr19-5692035-C-G
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_004793.4(LONP1):āc.2877G>Cā(p.Arg959=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000434 in 1,611,590 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 Likely benign (ā ). Synonymous variant affecting the same amino acid position (i.e. R959R) has been classified as Likely benign.
Frequency
Consequence
NM_004793.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LONP1 | NM_004793.4 | c.2877G>C | p.Arg959= | synonymous_variant | 18/18 | ENST00000360614.8 | |
LONP1 | NM_001276479.2 | c.2685G>C | p.Arg895= | synonymous_variant | 19/19 | ||
LONP1 | NM_001276480.1 | c.2289G>C | p.Arg763= | synonymous_variant | 18/18 | ||
LONP1 | NR_076392.2 | n.2682G>C | non_coding_transcript_exon_variant | 19/19 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LONP1 | ENST00000360614.8 | c.2877G>C | p.Arg959= | synonymous_variant | 18/18 | 1 | NM_004793.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152232Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.00000402 AC: 1AN: 248812Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 134562
GnomAD4 exome AF: 0.00000343 AC: 5AN: 1459358Hom.: 0 Cov.: 35 AF XY: 0.00000276 AC XY: 2AN XY: 725880
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152232Hom.: 0 Cov.: 34 AF XY: 0.0000134 AC XY: 1AN XY: 74370
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Oct 29, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at