rs201818201
Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS1
The NM_007327.4(GRIN1):āc.693A>Cā(p.Val231=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000795 in 1,599,020 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ). Synonymous variant affecting the same amino acid position (i.e. V231V) has been classified as Likely benign.
Frequency
Consequence
NM_007327.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -17 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GRIN1 | NM_007327.4 | c.693A>C | p.Val231= | synonymous_variant | 5/20 | ENST00000371561.8 | |
LOC105376328 | XR_007061876.1 | n.3239T>G | non_coding_transcript_exon_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GRIN1 | ENST00000371561.8 | c.693A>C | p.Val231= | synonymous_variant | 5/20 | 1 | NM_007327.4 |
Frequencies
GnomAD3 genomes ? AF: 0.000512 AC: 78AN: 152210Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.000542 AC: 120AN: 221366Hom.: 0 AF XY: 0.000574 AC XY: 69AN XY: 120138
GnomAD4 exome AF: 0.000825 AC: 1194AN: 1446692Hom.: 1 Cov.: 34 AF XY: 0.000860 AC XY: 618AN XY: 718348
GnomAD4 genome ? AF: 0.000512 AC: 78AN: 152328Hom.: 0 Cov.: 34 AF XY: 0.000564 AC XY: 42AN XY: 74492
ClinVar
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 16, 2021 | - - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Mar 01, 2024 | GRIN1: BP4, BP7 - |
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | May 03, 2016 | 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 8 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 08, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at