rs7604

Positions:

• chr6-38676020-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_006708.3(GLO1):​c.*1275G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.08 in 152,008 control chromosomes in the GnomAD database, including 652 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 0.080 (652 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: GLO1 NM_006708.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.453

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.112 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GLO1	NM_006708.3	c.*1275G>A		3_prime_UTR_variant	6/6	ENST00000373365.5	NP_006699.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GLO1	ENST00000373365	c.*1275G>A		3_prime_UTR_variant	6/6	1	NM_006708.3	ENSP00000362463.3
GLO1	ENST00000470973.1	n.1862G>A		non_coding_transcript_exon_variant	3/3	2

Frequencies

GnomAD3 genomes AF: 0.0801 AC: 12162 AN: 151890 Hom.: 652 Cov.: 32

Gnomad AFR AF: 0.0242

Gnomad AMI AF: 0.0362

Gnomad AMR AF: 0.0767

Gnomad ASJ AF: 0.184

Gnomad EAS AF: 0.00367

Gnomad SAS AF: 0.106

Gnomad FIN AF: 0.0723

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.114

Gnomad OTH AF: 0.0940

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.0800 AC: 12158 AN: 152008 Hom.: 652 Cov.: 32 AF XY: 0.0807 AC XY: 5996 AN XY: 74296

Gnomad4 AFR AF: 0.0242

Gnomad4 AMR AF: 0.0765

Gnomad4 ASJ AF: 0.184

Gnomad4 EAS AF: 0.00367

Gnomad4 SAS AF: 0.107

Gnomad4 FIN AF: 0.0723

Gnomad4 NFE AF: 0.114

Gnomad4 OTH AF: 0.0930

Alfa AF: 0.111 Hom.: 960

Bravo AF: 0.0767

Asia WGS AF: 0.0480 AC: 165 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	8.8
DANN	Benign	0.58
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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

LitVar

Other links and lift over

dbSNP: rs7604; hg19: chr6-38643796;