22-39970921-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_004810.4(GRAP2):c.830G>A(p.Arg277Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000746 in 1,608,654 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 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 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GRAP2 | NM_004810.4 | c.830G>A | p.Arg277Gln | missense_variant | 8/8 | ENST00000344138.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GRAP2 | ENST00000344138.9 | c.830G>A | p.Arg277Gln | missense_variant | 8/8 | 1 | NM_004810.4 | P1 | |
GRAP2 | ENST00000407075.3 | c.830G>A | p.Arg277Gln | missense_variant | 7/7 | 1 | P1 | ||
GRAP2 | ENST00000460449.1 | n.176G>A | non_coding_transcript_exon_variant | 2/2 | 2 |
Frequencies
GnomAD3 genomes AF: 0.000105 AC: 16AN: 152098Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000772 AC: 19AN: 246262Hom.: 1 AF XY: 0.0000824 AC XY: 11AN XY: 133464
GnomAD4 exome AF: 0.0000714 AC: 104AN: 1456438Hom.: 0 Cov.: 31 AF XY: 0.0000787 AC XY: 57AN XY: 724408
GnomAD4 genome AF: 0.000105 AC: 16AN: 152216Hom.: 0 Cov.: 32 AF XY: 0.0000672 AC XY: 5AN XY: 74426
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 03, 2021 | The c.830G>A (p.R277Q) alteration is located in exon 8 (coding exon 7) of the GRAP2 gene. This alteration results from a G to A substitution at nucleotide position 830, causing the arginine (R) at amino acid position 277 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