rs201592328
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 1P and 5B. PP2BP6BS1
The NM_007327.4(GRIN1):c.614C>T(p.Thr205Met) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000266 in 1,613,644 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. T205T) has been classified as Likely benign.
Frequency
Consequence
NM_007327.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GRIN1 | NM_007327.4 | c.614C>T | p.Thr205Met | missense_variant | 4/20 | ENST00000371561.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GRIN1 | ENST00000371561.8 | c.614C>T | p.Thr205Met | missense_variant | 4/20 | 1 | NM_007327.4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000394 AC: 6AN: 152240Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000923 AC: 23AN: 249240Hom.: 0 AF XY: 0.0000740 AC XY: 10AN XY: 135082
GnomAD4 exome AF: 0.0000253 AC: 37AN: 1461286Hom.: 0 Cov.: 31 AF XY: 0.0000248 AC XY: 18AN XY: 726918
GnomAD4 genome ? AF: 0.0000394 AC: 6AN: 152358Hom.: 0 Cov.: 33 AF XY: 0.0000671 AC XY: 5AN XY: 74510
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 10, 2022 | The c.614C>T (p.T205M) alteration is located in exon 4 (coding exon 4) of the GRIN1 gene. This alteration results from a C to T substitution at nucleotide position 614, causing the threonine (T) at amino acid position 205 to be replaced by a methionine (M). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Sep 15, 2020 | - - |
Intellectual disability, autosomal dominant 8 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 03, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at