rs192006771
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_ModerateBP6_Very_StrongBP7BS1
The NM_007327.4(GRIN1):c.246C>T(p.Leu82Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000273 in 1,613,666 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_007327.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -15 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152206Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000169 AC: 42AN: 248700Hom.: 0 AF XY: 0.000171 AC XY: 23AN XY: 134840
GnomAD4 exome AF: 0.0000246 AC: 36AN: 1461342Hom.: 0 Cov.: 32 AF XY: 0.0000248 AC XY: 18AN XY: 726988
GnomAD4 genome AF: 0.0000525 AC: 8AN: 152324Hom.: 0 Cov.: 32 AF XY: 0.0000671 AC XY: 5AN XY: 74476
ClinVar
Submissions by phenotype
Inborn genetic diseases Benign:1
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
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at