Genetic Variant GLO1:c.84+6153G>A (chr6-38696818-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is . The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_006708.3(GLO1):c.84+6153G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.183 in 152,110 control chromosomes in the GnomAD database, including 3,209 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 ( 3209 hom., cov: 32)

Consequence

GLO1
NM_006708.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0730

Publications

12 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:

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new If you want to explore the variant's impact on the transcript NM_006708.3, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

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=-0.97).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.267 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006708.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GLO1	NM_006708.3	MANE Select	c.84+6153G>A		intron	N/A	NP_006699.2	Q04760-1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
GLO1	ENST00000373365.5	TSL:1 MANE Select	c.84+6153G>A	intron	N/A	ENSP00000362463.3	Q04760-1
GLO1	ENST00000887179.1		c.84+6153G>A	intron	N/A	ENSP00000557238.1
GLO1	ENST00000887178.1		c.84+6153G>A	intron	N/A	ENSP00000557237.1

Frequencies

GnomAD3 genomes

AF:

0.183

AC:

27764

AN:

151996

Hom.:

3208

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0550

Gnomad AMI

AF:

0.444

Gnomad AMR

AF:

0.184

Gnomad ASJ

AF:

0.184

Gnomad EAS

AF:

0.0397

Gnomad SAS

AF:

0.113

Gnomad FIN

AF:

0.200

Gnomad MID

AF:

0.165

Gnomad NFE

AF:

0.270

Gnomad OTH

AF:

0.174

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.183

AC:

27764

AN:

152110

Hom.:

3209

Cov.:

AF XY:

0.176

AC XY:

13121

AN XY:

74362

show subpopulations

African (AFR)

AF:

0.0550

AC:

2283

AN:

41520

American (AMR)

AF:

0.183

AC:

2804

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.184

AC:

636

AN:

3464

East Asian (EAS)

AF:

0.0398

AC:

206

AN:

5182

South Asian (SAS)

AF:

0.114

AC:

548

AN:

4820

European-Finnish (FIN)

AF:

0.200

AC:

2107

AN:

10556

Middle Eastern (MID)

AF:

0.173

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.270

AC:

18360

AN:

67966

Other (OTH)

AF:

0.173

AC:

365

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1103

2207

3310

4414

5517

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

292

584

876

1168

1460

<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:

0.239

Hom.:

8295

Bravo

AF:

0.173

Asia WGS

AF:

0.0800

AC:

280

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

CADD

Benign

0.72

(source)

DANN

Benign

0.47

PhyloP100

-0.073

Mutation Taster

=100/0

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over