rs12986002
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_138690.3(GRIN3B):c.349C>T(p.His117Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.454 in 1,435,580 control chromosomes in the GnomAD database, including 151,015 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. H117L) has been classified as Uncertain significance.
Frequency
Consequence
NM_138690.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GRIN3B | NM_138690.3 | c.349C>T | p.His117Tyr | missense_variant | 1/9 | ENST00000234389.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GRIN3B | ENST00000234389.3 | c.349C>T | p.His117Tyr | missense_variant | 1/9 | 1 | NM_138690.3 | P1 | |
ENST00000588380.1 | n.270-619G>A | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.429 AC: 60701AN: 141380Hom.: 12872 Cov.: 30
GnomAD3 exomes AF: 0.419 AC: 24713AN: 59028Hom.: 5462 AF XY: 0.405 AC XY: 14374AN XY: 35488
GnomAD4 exome AF: 0.457 AC: 591176AN: 1294090Hom.: 138151 Cov.: 40 AF XY: 0.452 AC XY: 288290AN XY: 637648
GnomAD4 genome AF: 0.429 AC: 60697AN: 141490Hom.: 12864 Cov.: 30 AF XY: 0.425 AC XY: 29376AN XY: 69128
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 25, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at