chrX-123239256-C-T
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong
The NM_000828.5(GRIA3):c.269-14047C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.76 ( 22829 hom., 23658 hem., cov: 21)
Failed GnomAD Quality Control
Consequence
GRIA3
NM_000828.5 intron
NM_000828.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.199
Publications
4 publications found
Genes affected
GRIA3 (HGNC:4573): (glutamate ionotropic receptor AMPA type subunit 3) Glutamate receptors are the predominant excitatory neurotransmitter receptors in the mammalian brain and are activated in a variety of normal neurophysiologic processes. These receptors are heteromeric protein complexes composed of multiple subunits, arranged to form ligand-gated ion channels. The classification of glutamate receptors is based on their activation by different pharmacologic agonists. The subunit encoded by this gene belongs to a family of AMPA (alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate)-sensitive glutamate receptors, and is subject to RNA editing (AGA->GGA; R->G). Alternative splicing at this locus results in different isoforms, which may vary in their signal transduction properties. [provided by RefSeq, Jul 2008]
GRIA3 Gene-Disease associations (from GenCC):
- syndromic X-linked intellectual disability 94Inheritance: XL Classification: DEFINITIVE, STRONG, LIMITED Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae), G2P
- X-linked complex neurodevelopmental disorderInheritance: XL Classification: DEFINITIVE Submitted by: ClinGen
- X-linked intellectual disability due to GRIA3 anomaliesInheritance: XL Classification: SUPPORTIVE Submitted by: Orphanet
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -4 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GRIA3 | ENST00000620443.2 | c.269-14047C>T | intron_variant | Intron 2 of 15 | 1 | NM_007325.5 | ENSP00000478489.1 | |||
GRIA3 | ENST00000622768.5 | c.269-14047C>T | intron_variant | Intron 2 of 15 | 5 | NM_000828.5 | ENSP00000481554.1 |
Frequencies
GnomAD3 genomes AF: 0.757 AC: 82101AN: 108480Hom.: 22826 Cov.: 21 show subpopulations
GnomAD3 genomes
AF:
AC:
82101
AN:
108480
Hom.:
Cov.:
21
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
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Gnomad EAS
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Gnomad SAS
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Gnomad FIN
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Gnomad MID
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Gnomad NFE
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Gnomad OTH
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.757 AC: 82144AN: 108530Hom.: 22829 Cov.: 21 AF XY: 0.757 AC XY: 23658AN XY: 31264 show subpopulations
GnomAD4 genome
Data not reliable, filtered out with message: InbreedingCoeff
AF:
AC:
82144
AN:
108530
Hom.:
Cov.:
21
AF XY:
AC XY:
23658
AN XY:
31264
show subpopulations
African (AFR)
AF:
AC:
25640
AN:
30144
American (AMR)
AF:
AC:
8581
AN:
10207
Ashkenazi Jewish (ASJ)
AF:
AC:
1889
AN:
2549
East Asian (EAS)
AF:
AC:
3066
AN:
3428
South Asian (SAS)
AF:
AC:
1985
AN:
2435
European-Finnish (FIN)
AF:
AC:
3747
AN:
5648
Middle Eastern (MID)
AF:
AC:
145
AN:
191
European-Non Finnish (NFE)
AF:
AC:
35410
AN:
51780
Other (OTH)
AF:
AC:
1140
AN:
1480
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.503
Heterozygous variant carriers
0
681
1361
2042
2722
3403
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
678
1356
2034
2712
3390
<30
30-35
35-40
40-45
45-50
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65-70
70-75
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>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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