19-39435885-T-C
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_001020.6(RPS16):c.11A>G(p.Lys4Arg) variant causes a missense change. The variant allele was found at a frequency of 0.000192 in 1,606,316 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 (★).
Frequency
Consequence
NM_001020.6 missense
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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RPS16 | NM_001020.6 | c.11A>G | p.Lys4Arg | missense_variant | Exon 1 of 5 | ENST00000251453.8 | NP_001011.1 | |
RPS16 | NM_001363860.2 | c.11A>G | p.Lys4Arg | missense_variant | Exon 1 of 4 | NP_001350789.1 | ||
RPS16 | NM_001321111.2 | c.11A>G | p.Lys4Arg | missense_variant | Exon 1 of 5 | NP_001308040.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000105 AC: 16AN: 152248Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.0000734 AC: 18AN: 245204Hom.: 0 AF XY: 0.0000600 AC XY: 8AN XY: 133232
GnomAD4 exome AF: 0.000202 AC: 293AN: 1454068Hom.: 0 Cov.: 36 AF XY: 0.000200 AC XY: 145AN XY: 723816
GnomAD4 genome AF: 0.000105 AC: 16AN: 152248Hom.: 0 Cov.: 34 AF XY: 0.000108 AC XY: 8AN XY: 74382
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.11A>G (p.K4R) alteration is located in exon 1 (coding exon 1) of the RPS16 gene. This alteration results from a A to G substitution at nucleotide position 11, causing the lysine (K) at amino acid position 4 to be replaced by an arginine (R). 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