chr16-9754612-T-TG
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2
The NM_001134407.3(GRIN2A):c.*8536_*8537insC variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00896 in 216,630 control chromosomes in the GnomAD database, including 25 homozygotes. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.012 ( 22 hom., cov: 32)
Exomes 𝑓: 0.0025 ( 3 hom. )
Consequence
GRIN2A
NM_001134407.3 3_prime_UTR
NM_001134407.3 3_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -0.762
Genes affected
GRIN2A (HGNC:4585): (glutamate ionotropic receptor NMDA type subunit 2A) This gene encodes a member of the glutamate-gated ion channel protein family. The encoded protein is an N-methyl-D-aspartate (NMDA) receptor subunit. NMDA receptors are both ligand-gated and voltage-dependent, and are involved in long-term potentiation, an activity-dependent increase in the efficiency of synaptic transmission thought to underlie certain kinds of memory and learning. These receptors are permeable to calcium ions, and activation results in a calcium influx into post-synaptic cells, which results in the activation of several signaling cascades. Disruption of this gene is associated with focal epilepsy and speech disorder with or without cognitive disability. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2014]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP6
Variant 16-9754612-T-TG is Benign according to our data. Variant chr16-9754612-T-TG is described in ClinVar as [Likely_benign]. Clinvar id is 321470.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0117 (1784/152256) while in subpopulation AFR AF= 0.0402 (1671/41552). AF 95% confidence interval is 0.0386. There are 22 homozygotes in gnomad4. There are 862 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High AC in GnomAd4 at 1784 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GRIN2A | NM_001134407.3 | c.*8536_*8537insC | 3_prime_UTR_variant | 13/13 | ENST00000330684.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GRIN2A | ENST00000330684.4 | c.*8536_*8537insC | 3_prime_UTR_variant | 13/13 | 1 | NM_001134407.3 | P1 | ||
GRIN2A | ENST00000396573.6 | c.*8536_*8537insC | 3_prime_UTR_variant | 14/14 | 1 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0117 AC: 1777AN: 152138Hom.: 22 Cov.: 32
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GnomAD4 exome AF: 0.00245 AC: 158AN: 64374Hom.: 3 Cov.: 0 AF XY: 0.00201 AC XY: 60AN XY: 29778
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GnomAD4 genome AF: 0.0117 AC: 1784AN: 152256Hom.: 22 Cov.: 32 AF XY: 0.0116 AC XY: 862AN XY: 74464
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Landau-Kleffner syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Computational scores
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at