1-17438319-C-A
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_018715.4(RCC2):c.196G>T(p.Gly66Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000887 in 1,239,958 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G66D) has been classified 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.196G>T | p.Gly66Cys | missense_variant | Exon 2 of 13 | ENST00000375436.9 | NP_061185.1 | |
RCC2 | NM_001136204.3 | c.196G>T | p.Gly66Cys | missense_variant | Exon 1 of 12 | NP_001129676.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000201 AC: 3AN: 149460Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000734 AC: 8AN: 1090498Hom.: 0 Cov.: 30 AF XY: 0.00000567 AC XY: 3AN XY: 528852
GnomAD4 genome AF: 0.0000201 AC: 3AN: 149460Hom.: 0 Cov.: 32 AF XY: 0.0000412 AC XY: 3AN XY: 72890
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.196G>T (p.G66C) alteration is located in exon 2 (coding exon 1) of the RCC2 gene. This alteration results from a G to T substitution at nucleotide position 196, causing the glycine (G) at amino acid position 66 to be replaced by a cysteine (C). 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