6-42883610-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001366481.3(RPL7L1):c.307G>A(p.Glu103Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000258 in 1,589,020 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001366481.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RPL7L1 | NM_001366481.3 | c.307G>A | p.Glu103Lys | missense_variant | 3/6 | ENST00000493763.7 | NP_001353410.1 | |
RPL7L1 | NM_198486.5 | c.307G>A | p.Glu103Lys | missense_variant | 3/7 | NP_940888.3 | ||
RPL7L1 | NR_134562.3 | n.718G>A | non_coding_transcript_exon_variant | 3/7 | ||||
RPL7L1 | NR_134563.3 | n.496G>A | non_coding_transcript_exon_variant | 2/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RPL7L1 | ENST00000493763.7 | c.307G>A | p.Glu103Lys | missense_variant | 3/6 | 1 | NM_001366481.3 | ENSP00000418221.3 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152192Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000839 AC: 19AN: 226526Hom.: 0 AF XY: 0.0000653 AC XY: 8AN XY: 122512
GnomAD4 exome AF: 0.0000251 AC: 36AN: 1436828Hom.: 0 Cov.: 29 AF XY: 0.0000238 AC XY: 17AN XY: 713934
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152192Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74342
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 26, 2022 | The c.280G>A (p.E94K) alteration is located in exon 3 (coding exon 3) of the RPL7L1 gene. This alteration results from a G to A substitution at nucleotide position 280, causing the glutamic acid (E) at amino acid position 94 to be replaced by a lysine (K). 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