5-126483572-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_023927.4(GRAMD2B):c.845G>A(p.Arg282Gln) variant causes a missense, splice region change. The variant allele was found at a frequency of 0.000101 in 1,570,564 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/22 in silico tools predict a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_023927.4 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GRAMD2B | NM_023927.4 | c.845G>A | p.Arg282Gln | missense_variant, splice_region_variant | 9/14 | ENST00000285689.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GRAMD2B | ENST00000285689.8 | c.845G>A | p.Arg282Gln | missense_variant, splice_region_variant | 9/14 | 1 | NM_023927.4 | P1 | |
ENST00000648070.1 | n.705-15941C>T | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.0000264 AC: 4AN: 151776Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000728 AC: 18AN: 247302Hom.: 0 AF XY: 0.0000971 AC XY: 13AN XY: 133832
GnomAD4 exome AF: 0.000109 AC: 154AN: 1418788Hom.: 0 Cov.: 24 AF XY: 0.000107 AC XY: 76AN XY: 708258
GnomAD4 genome ? AF: 0.0000264 AC: 4AN: 151776Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74084
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 08, 2023 | The c.890G>A (p.R297Q) alteration is located in exon 9 (coding exon 9) of the GRAMD3 gene. This alteration results from a G to A substitution at nucleotide position 890, causing the arginine (R) at amino acid position 297 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