dbSNP rs1049346: GLO1: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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GLO1	NM_006708.3 link	c.-7C>T		5_prime_UTR_variant	Exon 1 of 6	ENST00000373365.5	NP_006699.2	Q04760-1X5DNM4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GLO1	ENST00000373365.5 link	c.-7C>T		5_prime_UTR_variant	Exon 1 of 6	1	NM_006708.3	ENSP00000362463.3		Q04760-1
ENSG00000298390	ENST00000755274.1 link	n.481-11173G>A		intron_variant	Intron 2 of 2

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 v4.3

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over