rs74759637
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_ModerateBS1
The NM_001510.4(GRID2):c.89-4C>G variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000561 in 1,603,424 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_001510.4 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GRID2 | ENST00000282020.9 | c.89-4C>G | splice_region_variant, intron_variant | Intron 1 of 15 | 1 | NM_001510.4 | ENSP00000282020.4 | |||
GRID2 | ENST00000510992.5 | c.89-4C>G | splice_region_variant, intron_variant | Intron 1 of 14 | 1 | ENSP00000421257.1 | ||||
GRID2 | ENST00000505687.5 | n.261-4C>G | splice_region_variant, intron_variant | Intron 1 of 5 | 1 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152108Hom.: 1 Cov.: 32
GnomAD4 exome AF: 0.00000276 AC: 4AN: 1451198Hom.: 0 Cov.: 28 AF XY: 0.00000277 AC XY: 2AN XY: 722510
GnomAD4 genome AF: 0.0000328 AC: 5AN: 152226Hom.: 1 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74416
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at