chr19-1003173-C-T
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_138690.3(GRIN3B):c.470C>T(p.Thr157Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.157 in 1,494,280 control chromosomes in the GnomAD database, including 21,279 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_138690.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GRIN3B | NM_138690.3 | c.470C>T | p.Thr157Met | missense_variant | 2/9 | ENST00000234389.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GRIN3B | ENST00000234389.3 | c.470C>T | p.Thr157Met | missense_variant | 2/9 | 1 | NM_138690.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.134 AC: 20448AN: 152124Hom.: 2000 Cov.: 34
GnomAD3 exomes AF: 0.189 AC: 24052AN: 127250Hom.: 3057 AF XY: 0.181 AC XY: 12711AN XY: 70216
GnomAD4 exome AF: 0.160 AC: 214664AN: 1342036Hom.: 19281 Cov.: 34 AF XY: 0.159 AC XY: 104691AN XY: 657204
GnomAD4 genome ? AF: 0.134 AC: 20441AN: 152244Hom.: 1998 Cov.: 34 AF XY: 0.137 AC XY: 10188AN XY: 74424
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at