chr3-6861471-TGGC-T
Position:
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 3P and 1B. PM2PM4_SupportingBS1_Supporting
The NM_000844.4(GRM7):βc.94_96delβ(p.Ala32del) variant causes a inframe deletion change. The variant allele was found at a frequency of 0.0000514 in 1,284,560 control chromosomes in the GnomAD database, including 1 homozygotes. Variant has been reported in ClinVar as Uncertain significance (β ).
Frequency
Genomes: π 0.000063 ( 0 hom., cov: 32)
Exomes π: 0.000050 ( 1 hom. )
Consequence
GRM7
NM_000844.4 inframe_deletion
NM_000844.4 inframe_deletion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 4.74
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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PM4
Nonframeshift variant in NON repetitive region in NM_000844.4. Strenght limited to Supporting due to length of the change: 1aa.
BS1
Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.0000632 (9/142492) while in subpopulation EAS AF= 0.000768 (3/3904). AF 95% confidence interval is 0.000209. There are 0 homozygotes in gnomad4. There are 5 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck. Existence of Clinvar submissions makes me limit the strength of this signal to Supporting
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GRM7 | NM_000844.4 | c.94_96del | p.Ala32del | inframe_deletion | 1/10 | ENST00000357716.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GRM7 | ENST00000357716.9 | c.94_96del | p.Ala32del | inframe_deletion | 1/10 | 1 | NM_000844.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000632 AC: 9AN: 142344Hom.: 0 Cov.: 32
GnomAD3 genomes
AF:
AC:
9
AN:
142344
Hom.:
Cov.:
32
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:
GnomAD3 exomes AF: 0.0000966 AC: 20AN: 206984Hom.: 1 AF XY: 0.0000701 AC XY: 8AN XY: 114140
GnomAD3 exomes
AF:
AC:
20
AN:
206984
Hom.:
AF XY:
AC XY:
8
AN XY:
114140
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.0000499 AC: 57AN: 1142068Hom.: 1 AF XY: 0.0000405 AC XY: 23AN XY: 568466
GnomAD4 exome
AF:
AC:
57
AN:
1142068
Hom.:
AF XY:
AC XY:
23
AN XY:
568466
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome AF: 0.0000632 AC: 9AN: 142492Hom.: 0 Cov.: 32 AF XY: 0.0000722 AC XY: 5AN XY: 69292
GnomAD4 genome
AF:
AC:
9
AN:
142492
Hom.:
Cov.:
32
AF XY:
AC XY:
5
AN XY:
69292
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Mar 04, 2022 | This variant, c.94_96del, results in the deletion of 1 amino acid(s) of the GRM7 protein (p.Ala32del), but otherwise preserves the integrity of the reading frame. The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This variant has not been reported in the literature in individuals affected with GRM7-related conditions. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
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