chr22-39971025-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_004810.4(GRAP2):c.934C>T(p.Arg312Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000104 in 1,613,806 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_004810.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GRAP2 | NM_004810.4 | c.934C>T | p.Arg312Cys | missense_variant | 8/8 | ENST00000344138.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GRAP2 | ENST00000344138.9 | c.934C>T | p.Arg312Cys | missense_variant | 8/8 | 1 | NM_004810.4 | P1 | |
GRAP2 | ENST00000407075.3 | c.934C>T | p.Arg312Cys | missense_variant | 7/7 | 1 | P1 | ||
GRAP2 | ENST00000460449.1 | n.280C>T | non_coding_transcript_exon_variant | 2/2 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000854 AC: 13AN: 152150Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000104 AC: 26AN: 250978Hom.: 0 AF XY: 0.0000958 AC XY: 13AN XY: 135682
GnomAD4 exome AF: 0.000107 AC: 156AN: 1461538Hom.: 0 Cov.: 31 AF XY: 0.000105 AC XY: 76AN XY: 727090
GnomAD4 genome ? AF: 0.0000788 AC: 12AN: 152268Hom.: 0 Cov.: 32 AF XY: 0.0000672 AC XY: 5AN XY: 74440
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 11, 2021 | The c.934C>T (p.R312C) alteration is located in exon 8 (coding exon 7) of the GRAP2 gene. This alteration results from a C to T substitution at nucleotide position 934, causing the arginine (R) at amino acid position 312 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