chr19-48398491-G-C
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_000836.4(GRIN2D):c.99G>C(p.Pro33=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. P33P) has been classified as Likely benign.
Frequency
Consequence
NM_000836.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GRIN2D | NM_000836.4 | c.99G>C | p.Pro33= | synonymous_variant | 3/14 | ENST00000263269.4 | |
GRIN2D | XM_011526872.2 | c.99G>C | p.Pro33= | synonymous_variant | 1/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GRIN2D | ENST00000263269.4 | c.99G>C | p.Pro33= | synonymous_variant | 3/14 | 1 | NM_000836.4 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 30
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 864538Hom.: 0 Cov.: 28 AF XY: 0.00 AC XY: 0AN XY: 402164
GnomAD4 genome ? Cov.: 30
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Sep 30, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.