chr4-108622515-G-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The ENST00000394667.8(RPL34):c.166G>A(p.Val56Ile) variant causes a missense, splice region change. The variant allele was found at a frequency of 0.000227 in 1,607,038 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/22 in silico tools predict a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
ENST00000394667.8 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RPL34 | NM_001319236.2 | c.166G>A | p.Val56Ile | missense_variant, splice_region_variant | 4/5 | ENST00000394667.8 | NP_001306165.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RPL34 | ENST00000394667.8 | c.166G>A | p.Val56Ile | missense_variant, splice_region_variant | 4/5 | 1 | NM_001319236.2 | ENSP00000378162 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000920 AC: 14AN: 152154Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000443 AC: 11AN: 248102Hom.: 0 AF XY: 0.0000373 AC XY: 5AN XY: 134048
GnomAD4 exome AF: 0.000241 AC: 351AN: 1454884Hom.: 0 Cov.: 28 AF XY: 0.000238 AC XY: 172AN XY: 724052
GnomAD4 genome AF: 0.0000920 AC: 14AN: 152154Hom.: 0 Cov.: 33 AF XY: 0.0000538 AC XY: 4AN XY: 74344
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 15, 2023 | The c.166G>A (p.V56I) alteration is located in exon 4 (coding exon 3) of the RPL34 gene. This alteration results from a G to A substitution at nucleotide position 166, causing the valine (V) at amino acid position 56 to be replaced by an isoleucine (I). 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