Genetic Variant NM_006708.3:c.-7C>T (chr6-38703061-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_006708.3(GLO1):c.-7C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.485 in 1,517,806 control chromosomes in the GnomAD database, including 181,471 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 0.54 ( 22719 hom., cov: 33)

Exomes 𝑓: 0.48 ( 158752 hom. )

Consequence

GLO1
NM_006708.3 5_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.632

Publications

42 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 -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.72).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.668 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.-7C>T		5_prime_UTR	Exon 1 of 6	NP_006699.2	Q04760-1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
GLO1	ENST00000373365.5	TSL:1 MANE Select	c.-7C>T	5_prime_UTR	Exon 1 of 6	ENSP00000362463.3	Q04760-1
GLO1	ENST00000887179.1		c.-7C>T	5_prime_UTR	Exon 1 of 7	ENSP00000557238.1
GLO1	ENST00000887178.1		c.-7C>T	5_prime_UTR	Exon 1 of 6	ENSP00000557237.1

Frequencies

GnomAD3 genomes

AF:

0.538

AC:

81834

AN:

152002

Hom.:

22696

Cov.:

show subpopulations

Gnomad AFR

AF:

0.675

Gnomad AMI

AF:

0.690

Gnomad AMR

AF:

0.502

Gnomad ASJ

AF:

0.483

Gnomad EAS

AF:

0.612

Gnomad SAS

AF:

0.508

Gnomad FIN

AF:

0.383

Gnomad MID

AF:

0.443

Gnomad NFE

AF:

0.486

Gnomad OTH

AF:

0.511

GnomAD2 exomes

AF:

0.495

AC:

115352

AN:

233028

AF XY:

0.494

show subpopulations

Gnomad AFR exome

AF:

0.677

Gnomad AMR exome

AF:

0.445

Gnomad ASJ exome

AF:

0.490

Gnomad EAS exome

AF:

0.622

Gnomad FIN exome

AF:

0.390

Gnomad NFE exome

AF:

0.480

Gnomad OTH exome

AF:

0.486

GnomAD4 exome

AF:

0.479

AC:

653923

AN:

1365686

Hom.:

158752

Cov.:

AF XY:

0.480

AC XY:

328235

AN XY:

684302

show subpopulations

African (AFR)

AF:

0.674

AC:

20404

AN:

30270

American (AMR)

AF:

0.455

AC:

19101

AN:

42020

Ashkenazi Jewish (ASJ)

AF:

0.489

AC:

12352

AN:

25284

East Asian (EAS)

AF:

0.580

AC:

22312

AN:

38452

South Asian (SAS)

AF:

0.511

AC:

42929

AN:

84008

European-Finnish (FIN)

AF:

0.401

AC:

21051

AN:

52504

Middle Eastern (MID)

AF:

0.498

AC:

2776

AN:

5570

European-Non Finnish (NFE)

AF:

0.470

AC:

484862

AN:

1030696

Other (OTH)

AF:

0.495

AC:

28136

AN:

56882

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.449

Heterozygous variant carriers

13428

26856

40283

53711

67139

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

14004

28008

42012

56016

70020

<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:

0.538

AC:

81907

AN:

152120

Hom.:

22719

Cov.:

AF XY:

0.533

AC XY:

39634

AN XY:

74362

show subpopulations

African (AFR)

AF:

0.675

AC:

28029

AN:

41530

American (AMR)

AF:

0.502

AC:

7671

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.483

AC:

1676

AN:

3470

East Asian (EAS)

AF:

0.611

AC:

3141

AN:

5142

South Asian (SAS)

AF:

0.506

AC:

2443

AN:

4824

European-Finnish (FIN)

AF:

0.383

AC:

4054

AN:

10578

Middle Eastern (MID)

AF:

0.439

AC:

129

AN:

294

European-Non Finnish (NFE)

AF:

0.486

AC:

33058

AN:

67976

Other (OTH)

AF:

0.511

AC:

1078

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1937

3874

5811

7748

9685

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

708

1416

2124

2832

3540

<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:

0.499

Hom.:

77352

Bravo

AF:

0.551

Asia WGS

AF:

0.538

AC:

1870

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.72

CADD

Benign

3.2

(source)

DANN

Benign

0.81

PhyloP100

-0.63

PromoterAI

-0.12

Neutral

(source)

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Mutation Taster

=300/0

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

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

Computational scores

Splicing

Publications

Other links and lift over