Genetic Variant NM_001278064.2:c.2651G>A (chr6-146399690-G-A) – ACMG Classification: Benign (-20 pts)

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2

The NM_001278064.2(GRM1):c.2651G>A(p.Gly884Glu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0168 in 1,607,602 control chromosomes in the GnomAD database, including 331 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.013 ( 22 hom., cov: 32)

Exomes 𝑓: 0.017 ( 309 hom. )

Consequence

GRM1
NM_001278064.2 missense

Scores

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:6

Conservation

PhyloP100: 7.76

Publications

14 publications found

Variant links:

Genes affected

GRM1 (HGNC:4593): (glutamate metabotropic receptor 1) This gene encodes a metabotropic glutamate receptor that functions by activating phospholipase C. L-glutamate is the major excitatory neurotransmitter in the central nervous system and 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 canonical alpha isoform of the encoded protein is a disulfide-linked homodimer whose activity is mediated by a G-protein-coupled phosphatidylinositol-calcium second messenger system. This gene may be associated with many disease states, including schizophrenia, bipolar disorder, depression, and breast cancer. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, May 2013]

GRM1 Gene-Disease associations (from GenCC):

spinocerebellar ataxia 44
Inheritance: AD Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)
autosomal recessive spinocerebellar ataxia 13
Inheritance: AR Classification: STRONG, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), Orphanet, G2P

GRM1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0066556633).

BP6

Variant 6-146399690-G-A is Benign according to our data. Variant chr6-146399690-G-A is described in ClinVar as Benign/Likely_benign. ClinVar VariationId is 995113.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS1

Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0134 (2033/152212) while in subpopulation NFE AF = 0.0189 (1282/68008). AF 95% confidence interval is 0.018. There are 22 homozygotes in GnomAd4. There are 1019 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.

BS2

High Homozygotes in GnomAd4 at 22 AR,AD gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001278064.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein
GRM1	NM_001278064.2	MANE Select	c.2651G>A	p.Gly884Glu	missense	Exon 7 of 8	NP_001264993.1
GRM1	NM_001278067.1		c.2651G>A	p.Gly884Glu	missense	Exon 7 of 8	NP_001264996.1
GRM1	NM_001278065.2		c.2651G>A	p.Gly884Glu	missense	Exon 8 of 10	NP_001264994.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein
GRM1	ENST00000282753.6	TSL:1 MANE Select	c.2651G>A	p.Gly884Glu	missense	Exon 7 of 8	ENSP00000282753.1
GRM1	ENST00000355289.8	TSL:1	c.2651G>A	p.Gly884Glu	missense	Exon 7 of 8	ENSP00000347437.4
GRM1	ENST00000492807.6	TSL:1	c.2651G>A	p.Gly884Glu	missense	Exon 8 of 10	ENSP00000424095.1

Frequencies

GnomAD3 genomes

AF:

0.0134

AC:

2033

AN:

152094

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00270

Gnomad AMI

AF:

0.0110

Gnomad AMR

AF:

0.00707

Gnomad ASJ

AF:

0.00922

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00125

Gnomad FIN

AF:

0.0439

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.0188

Gnomad OTH

AF:

0.00814

GnomAD2 exomes

AF:

0.0164

AC:

3992

AN:

243170

AF XY:

0.0164

show subpopulations

Gnomad AFR exome

AF:

0.00287

Gnomad AMR exome

AF:

0.00511

Gnomad ASJ exome

AF:

0.0116

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.0471

Gnomad NFE exome

AF:

0.0237

Gnomad OTH exome

AF:

0.0179

GnomAD4 exome

AF:

0.0172

AC:

24981

AN:

1455390

Hom.:

309

Cov.:

AF XY:

0.0167

AC XY:

12082

AN XY:

724164

show subpopulations

African (AFR)

AF:

0.00240

AC:

AN:

33396

American (AMR)

AF:

0.00545

AC:

243

AN:

44586

Ashkenazi Jewish (ASJ)

AF:

0.0128

AC:

335

AN:

26086

East Asian (EAS)

AF:

0.0000504

AC:

AN:

39676

South Asian (SAS)

AF:

0.000651

AC:

AN:

86000

European-Finnish (FIN)

AF:

0.0483

AC:

2465

AN:

50998

Middle Eastern (MID)

AF:

0.00189

AC:

AN:

5302

European-Non Finnish (NFE)

AF:

0.0189

AC:

20935

AN:

1109170

Other (OTH)

AF:

0.0142

AC:

855

AN:

60176

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.476

Heterozygous variant carriers

1182

2363

3545

4726

5908

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

736

1472

2208

2944

3680

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0134

AC:

2033

AN:

152212

Hom.:

Cov.:

AF XY:

0.0137

AC XY:

1019

AN XY:

74422

show subpopulations

African (AFR)

AF:

0.00270

AC:

112

AN:

41542

American (AMR)

AF:

0.00706

AC:

108

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.00922

AC:

AN:

3472

East Asian (EAS)

AF:

0.00

AC:

AN:

5168

South Asian (SAS)

AF:

0.00125

AC:

AN:

4812

European-Finnish (FIN)

AF:

0.0439

AC:

465

AN:

10598

Middle Eastern (MID)

AF:

0.00340

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0189

AC:

1282

AN:

68008

Other (OTH)

AF:

0.00806

AC:

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

100

201

301

402

502

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

120

<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:

0.0162

Hom.:

Bravo

AF:

0.0102

TwinsUK

AF:

0.0140

AC:

ALSPAC

AF:

0.0169

AC:

ESP6500AA

AF:

0.00250

AC:

ESP6500EA

AF:

0.0147

AC:

126

ExAC

AF:

0.0182

AC:

2210

Asia WGS

AF:

0.000577

AC:

AN:

3478

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:6

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Jan 20, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

May 06, 2021

GeneDx

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

Breakthrough Genomics, Breakthrough Genomics

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:not provided

not specified

Benign:1

Dec 05, 2023

Athena Diagnostics

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

Autosomal recessive spinocerebellar ataxia 13;C4521563:Spinocerebellar ataxia 44

Benign:1

Dec 02, 2021

Fulgent Genetics, Fulgent Genetics

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

Autosomal recessive spinocerebellar ataxia 13

Benign:1

Jul 17, 2023

Victorian Clinical Genetics Services, Murdoch Childrens Research Institute

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as likely benign. Following criteria are met: 0308 - Population frequency for this variant is out of keeping with known incidence of spinocerebellar ataxia, autosomal recessive 13 (MIM#614831), with 77 homozygotes in gnomAD v2. (SB) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.13

BayesDel_addAF

Benign

-0.27

BayesDel_noAF

Benign

-0.14

CADD

Uncertain

(source)

DANN

Uncertain

0.98

DEOGEN2

Benign

0.072

Eigen

Uncertain

0.25

Eigen_PC

Uncertain

0.38

FATHMM_MKL

Pathogenic

0.99

LIST_S2

Benign

0.70

MetaRNN

Benign

0.0067

MetaSVM

Uncertain

-0.14

MutationAssessor

Benign

1.9

PhyloP100

7.8

PrimateAI

Uncertain

0.68

PROVEAN

Benign

-0.32

REVEL

Uncertain

0.33

Sift

Benign

0.12

Sift4G

Benign

0.11

Polyphen

0.98

Vest4

0.21

MPC

0.90

ClinPred

0.037

GERP RS

5.7

Varity_R

0.32

gMVP

0.40

Mutation Taster

=91/9

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over