Genetic Variant NM_006708.3:c.372A>T (chr6-38682812-T-A) – ACMG Classification: Benign (-11 pts)

Variant summary

Our verdict is Benign. The variant received -11 ACMG points: 0P and 11B. BP4_ModerateBP7BA1

The NM_006708.3(GLO1):c.372A>T(p.Gly124Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.13 in 1,575,686 control chromosomes in the GnomAD database, including 16,596 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 0.18 ( 3112 hom., cov: 32)

Exomes 𝑓: 0.12 ( 13484 hom. )

Consequence

GLO1
NM_006708.3 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.291

Publications

30 publications found

Variant links:

Genes affected

GLO1 (HGNC:4323): (glyoxalase I) The enzyme encoded by this gene is responsible for the catalysis and formation of S-lactoyl-glutathione from methylglyoxal condensation and reduced glutatione. Glyoxalase I is linked to HLA and is localized to 6p21.3-p21.1, between HLA and the centromere. [provided by RefSeq, Jul 2008]

GLO1 links:

ENSG00000298390 (HGNC:):

ENSG00000298390 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.37).

BP7

Synonymous conserved (PhyloP=0.291 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.304 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GLO1	NM_006708.3 link	c.372A>T	p.Gly124Gly	synonymous_variant	Exon 4 of 6	ENST00000373365.5	NP_006699.2	Q04760-1X5DNM4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
GLO1	ENST00000373365.5 link	c.372A>T	p.Gly124Gly	synonymous_variant	Exon 4 of 6	1	NM_006708.3	ENSP00000362463.3	Q04760-1
GLO1	ENST00000470973.1 link	n.404A>T		non_coding_transcript_exon_variant	Exon 1 of 3	2
ENSG00000298390	ENST00000755274.1 link	n.480+28145T>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.181

AC:

27537

AN:

151920

Hom.:

3111

Cov.:

show subpopulations

Gnomad AFR

AF:

0.308

Gnomad AMI

AF:

0.0987

Gnomad AMR

AF:

0.157

Gnomad ASJ

AF:

0.234

Gnomad EAS

AF:

0.232

Gnomad SAS

AF:

0.244

Gnomad FIN

AF:

0.0884

Gnomad MID

AF:

0.212

Gnomad NFE

AF:

0.114

Gnomad OTH

AF:

0.173

GnomAD2 exomes

AF:

0.159

AC:

39850

AN:

251310

AF XY:

0.161

show subpopulations

Gnomad AFR exome

AF:

0.314

Gnomad AMR exome

AF:

0.134

Gnomad ASJ exome

AF:

0.230

Gnomad EAS exome

AF:

0.237

Gnomad FIN exome

AF:

0.0851

Gnomad NFE exome

AF:

0.115

Gnomad OTH exome

AF:

0.148

GnomAD4 exome

AF:

0.125

AC:

177800

AN:

1423648

Hom.:

13484

Cov.:

AF XY:

0.129

AC XY:

91428

AN XY:

710958

show subpopulations

African (AFR)

AF:

0.317

AC:

10356

AN:

32626

American (AMR)

AF:

0.138

AC:

6145

AN:

44666

Ashkenazi Jewish (ASJ)

AF:

0.231

AC:

5968

AN:

25860

East Asian (EAS)

AF:

0.205

AC:

8076

AN:

39470

South Asian (SAS)

AF:

0.249

AC:

21258

AN:

85384

European-Finnish (FIN)

AF:

0.0882

AC:

4706

AN:

53386

Middle Eastern (MID)

AF:

0.226

AC:

1288

AN:

5700

European-Non Finnish (NFE)

AF:

0.103

AC:

111378

AN:

1077478

Other (OTH)

AF:

0.146

AC:

8625

AN:

59078

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.488

Heterozygous variant carriers

6926

13852

20779

27705

34631

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

4202

8404

12606

16808

21010

<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:

0.181

AC:

27559

AN:

152038

Hom.:

3112

Cov.:

AF XY:

0.182

AC XY:

13530

AN XY:

74328

show subpopulations

African (AFR)

AF:

0.308

AC:

12761

AN:

41402

American (AMR)

AF:

0.157

AC:

2401

AN:

15270

Ashkenazi Jewish (ASJ)

AF:

0.234

AC:

812

AN:

3468

East Asian (EAS)

AF:

0.231

AC:

1198

AN:

5178

South Asian (SAS)

AF:

0.243

AC:

1173

AN:

4820

European-Finnish (FIN)

AF:

0.0884

AC:

935

AN:

10580

Middle Eastern (MID)

AF:

0.194

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.114

AC:

7771

AN:

68008

Other (OTH)

AF:

0.171

AC:

361

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1090

2181

3271

4362

5452

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

300

600

900

1200

1500

<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:

0.144

Hom.:

622

Bravo

AF:

0.190

Asia WGS

AF:

0.217

AC:

751

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.37

CADD

Benign

7.0

(source)

DANN

Benign

0.57

PhyloP100

0.29

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Mutation Taster

=96/4

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over