5-145859871-C-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_001080516.2(GRXCR2):c.609G>A(p.Ser203Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000723 in 1,603,708 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 Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. S203S) has been classified as Likely benign.
Frequency
Consequence
NM_001080516.2 synonymous
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GRXCR2 | ENST00000377976.3 | c.609G>A | p.Ser203Ser | synonymous_variant | Exon 3 of 3 | 2 | NM_001080516.2 | ENSP00000367214.1 | ||
GRXCR2 | ENST00000639411.1 | c.204G>A | p.Ser68Ser | synonymous_variant | Exon 4 of 4 | 5 | ENSP00000491860.1 |
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152192Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000533 AC: 13AN: 243908Hom.: 0 AF XY: 0.0000531 AC XY: 7AN XY: 131794
GnomAD4 exome AF: 0.0000744 AC: 108AN: 1451516Hom.: 0 Cov.: 31 AF XY: 0.0000749 AC XY: 54AN XY: 720934
GnomAD4 genome AF: 0.0000526 AC: 8AN: 152192Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74340
ClinVar
Submissions by phenotype
not provided Benign:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at