1-17425618-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_018715.4(RCC2):c.446G>A(p.Arg149Gln) variant causes a missense change. The variant allele was found at a frequency of 0.000116 in 1,614,000 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_018715.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RCC2 | NM_018715.4 | c.446G>A | p.Arg149Gln | missense_variant | Exon 4 of 13 | ENST00000375436.9 | NP_061185.1 | |
RCC2 | NM_001136204.3 | c.446G>A | p.Arg149Gln | missense_variant | Exon 3 of 12 | NP_001129676.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000854 AC: 13AN: 152188Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000120 AC: 30AN: 250620Hom.: 0 AF XY: 0.000125 AC XY: 17AN XY: 135632
GnomAD4 exome AF: 0.000119 AC: 174AN: 1461812Hom.: 0 Cov.: 32 AF XY: 0.0000908 AC XY: 66AN XY: 727206
GnomAD4 genome AF: 0.0000854 AC: 13AN: 152188Hom.: 0 Cov.: 33 AF XY: 0.0000673 AC XY: 5AN XY: 74326
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.446G>A (p.R149Q) alteration is located in exon 4 (coding exon 3) of the RCC2 gene. This alteration results from a G to A substitution at nucleotide position 446, causing the arginine (R) at amino acid position 149 to be replaced by a glutamine (Q). 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