17-74842556-AGCCCCAGAGTCCTGCCCCTGT-A
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 2P and 9B. PM4BP6BS1BS2
The NM_000835.6(GRIN2C):c.3560_3580delACAGGGGCAGGACTCTGGGGC(p.His1187_Gly1193del) variant causes a disruptive inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00213 in 777,666 control chromosomes in the GnomAD database, including 21 homozygotes. Variant has been reported in ClinVar as Benign (no stars).
Frequency
Consequence
NM_000835.6 disruptive_inframe_deletion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GRIN2C | NM_000835.6 | c.3560_3580delACAGGGGCAGGACTCTGGGGC | p.His1187_Gly1193del | disruptive_inframe_deletion | Exon 13 of 13 | ENST00000293190.10 | NP_000826.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00698 AC: 1061AN: 151974Hom.: 16 Cov.: 34
GnomAD3 exomes AF: 0.00155 AC: 372AN: 240596Hom.: 4 AF XY: 0.00128 AC XY: 168AN XY: 131522
GnomAD4 exome AF: 0.000948 AC: 593AN: 625574Hom.: 5 AF XY: 0.000816 AC XY: 278AN XY: 340740
GnomAD4 genome AF: 0.00698 AC: 1061AN: 152092Hom.: 16 Cov.: 34 AF XY: 0.00679 AC XY: 505AN XY: 74370
ClinVar
Submissions by phenotype
GRIN2C-related disorder Benign:1
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at