rs524874
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001143831.3(GRM5):c.661+67997T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.615 in 152,006 control chromosomes in the GnomAD database, including 30,258 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 0.62 ( 30258 hom., cov: 31)
Consequence
GRM5
NM_001143831.3 intron
NM_001143831.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.41
Genes affected
GRM5 (HGNC:4597): (glutamate metabotropic receptor 5) This gene encodes a member of the G-protein coupled receptor 3 protein family. The encoded protein is a metabatropic glutamate receptor, whose signaling activates a phosphatidylinositol-calcium second messenger system. This protein may be involved in the regulation of neural network activity and synaptic plasticity. Glutamatergic neurotransmission is involved in most aspects of normal brain function and can be perturbed in many neuropathologic conditions. A pseudogene of this gene has been defined on chromosome 11. 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 -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.99).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.817 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GRM5 | NM_001143831.3 | c.661+67997T>C | intron_variant | ENST00000305447.5 | |||
GRM5 | NM_000842.5 | c.661+67997T>C | intron_variant | ||||
GRM5 | NM_001384268.1 | c.661+67997T>C | intron_variant | ||||
GRM5 | XM_011542792.2 | c.661+67997T>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GRM5 | ENST00000305447.5 | c.661+67997T>C | intron_variant | 1 | NM_001143831.3 | A2 | |||
GRM5 | ENST00000305432.9 | c.661+67997T>C | intron_variant | 1 | P2 | ||||
GRM5 | ENST00000449371.6 | c.223+29820T>C | intron_variant | 3 | |||||
GRM5 | ENST00000455756.6 | c.661+67997T>C | intron_variant | 2 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.615 AC: 93396AN: 151888Hom.: 30212 Cov.: 31
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.615 AC: 93496AN: 152006Hom.: 30258 Cov.: 31 AF XY: 0.610 AC XY: 45288AN XY: 74302
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45288
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74302
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2167
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at