rs78765966
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_000834.5(GRIN2B):c.3807A>T(p.Pro1269Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000773 in 1,614,152 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_000834.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GRIN2B | NM_000834.5 | c.3807A>T | p.Pro1269Pro | synonymous_variant | Exon 14 of 14 | ENST00000609686.4 | NP_000825.2 | |
GRIN2B | NM_001413992.1 | c.3807A>T | p.Pro1269Pro | synonymous_variant | Exon 15 of 15 | NP_001400921.1 | ||
GRIN2B | XM_005253351.3 | c.1593A>T | p.Pro531Pro | synonymous_variant | Exon 4 of 4 | XP_005253408.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GRIN2B | ENST00000609686.4 | c.3807A>T | p.Pro1269Pro | synonymous_variant | Exon 14 of 14 | 1 | NM_000834.5 | ENSP00000477455.1 | ||
GRIN2B | ENST00000637214.1 | c.69+45172A>T | intron_variant | Intron 1 of 1 | 5 | ENSP00000489997.1 |
Frequencies
GnomAD3 genomes AF: 0.000539 AC: 82AN: 152142Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000525 AC: 132AN: 251442Hom.: 0 AF XY: 0.000574 AC XY: 78AN XY: 135896
GnomAD4 exome AF: 0.000796 AC: 1164AN: 1461892Hom.: 2 Cov.: 33 AF XY: 0.000802 AC XY: 583AN XY: 727246
GnomAD4 genome AF: 0.000545 AC: 83AN: 152260Hom.: 0 Cov.: 33 AF XY: 0.000524 AC XY: 39AN XY: 74442
ClinVar
Submissions by phenotype
not provided Benign:4
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GRIN2B: BP4, BP7 -
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not specified Benign:1
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
Inborn genetic diseases Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Intellectual disability, autosomal dominant 6;C4015316:Developmental and epileptic encephalopathy, 27 Benign:1
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GRIN2B-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at