rs12489404
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_000844.4(GRM7):c.879-1487C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.474 in 151,972 control chromosomes in the GnomAD database, including 18,743 homozygotes. 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 0.47 ( 18743 hom., cov: 31)
Consequence
GRM7
NM_000844.4 intron
NM_000844.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.627
Publications
2 publications found
Genes affected
GRM7 (HGNC:4599): (glutamate metabotropic receptor 7) L-glutamate is the major excitatory neurotransmitter in the central nervous system, and it activates both ionotropic and metabotropic glutamate receptors. Glutamatergic neurotransmission is involved in most aspects of normal brain function and can be perturbed in many neuropathologic conditions. The metabotropic glutamate receptors are a family of G protein-coupled receptors that have been divided into three groups on the basis of sequence homology, putative signal transduction mechanisms, and pharmacologic properties. Group I includes GRM1 and GRM5, and these receptors have been shown to activate phospholipase C. Group II includes GRM2 and GRM3, while Group III includes GRM4, GRM6, GRM7 and GRM8. Group II and III receptors are linked to the inhibition of the cyclic AMP cascade but differ in their agonist selectivities. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jun 2009]
GRM7 Gene-Disease associations (from GenCC):
- neurodevelopmental disorder with seizures, hypotonia, and brain imaging abnormalitiesInheritance: AR Classification: STRONG, MODERATE Submitted by: G2P, Labcorp Genetics (formerly Invitae), Ambry Genetics
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.595 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.474 AC: 71996AN: 151854Hom.: 18748 Cov.: 31 show subpopulations
GnomAD3 genomes
AF:
AC:
71996
AN:
151854
Hom.:
Cov.:
31
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.474 AC: 71998AN: 151972Hom.: 18743 Cov.: 31 AF XY: 0.471 AC XY: 34965AN XY: 74258 show subpopulations
GnomAD4 genome
AF:
AC:
71998
AN:
151972
Hom.:
Cov.:
31
AF XY:
AC XY:
34965
AN XY:
74258
show subpopulations
African (AFR)
AF:
AC:
10659
AN:
41470
American (AMR)
AF:
AC:
6292
AN:
15258
Ashkenazi Jewish (ASJ)
AF:
AC:
1972
AN:
3470
East Asian (EAS)
AF:
AC:
2416
AN:
5146
South Asian (SAS)
AF:
AC:
2470
AN:
4820
European-Finnish (FIN)
AF:
AC:
5667
AN:
10554
Middle Eastern (MID)
AF:
AC:
163
AN:
294
European-Non Finnish (NFE)
AF:
AC:
40732
AN:
67946
Other (OTH)
AF:
AC:
1087
AN:
2108
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
1814
3627
5441
7254
9068
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
652
1304
1956
2608
3260
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
1784
AN:
3478
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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