rs3799703

chr6-38678854-A-G

Variant summary

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

The NM_006708.3(GLO1):c.467-1471T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.488 in 151,730 control chromosomes in the GnomAD database, including 18,347 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 0.49 (18347 hom., cov: 31)
• Consequence: GLO1 NM_006708.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0470

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.532 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GLO1	NM_006708.3	c.467-1471T>C		intron_variant		ENST00000373365.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GLO1	ENST00000373365.5	c.467-1471T>C		intron_variant		1	NM_006708.3	P1
GLO1	ENST00000470973.1	n.499-1471T>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.488 AC: 73965 AN: 151612 Hom.: 18343 Cov.: 31

Gnomad AFR AF: 0.462

Gnomad AMI AF: 0.520

Gnomad AMR AF: 0.476

Gnomad ASJ AF: 0.536

Gnomad EAS AF: 0.276

Gnomad SAS AF: 0.415

Gnomad FIN AF: 0.417

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.536

Gnomad OTH AF: 0.460

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

GnomAD4 genome AF: 0.488 AC: 73999 AN: 151730 Hom.: 18347 Cov.: 31 AF XY: 0.481 AC XY: 35704 AN XY: 74160

Gnomad4 AFR AF: 0.462

Gnomad4 AMR AF: 0.475

Gnomad4 ASJ AF: 0.536

Gnomad4 EAS AF: 0.276

Gnomad4 SAS AF: 0.416

Gnomad4 FIN AF: 0.417

Gnomad4 NFE AF: 0.536

Gnomad4 OTH AF: 0.455

Alfa AF: 0.507 Hom.: 9987

Bravo AF: 0.484

Asia WGS AF: 0.337 AC: 1172 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	2.2
Dann	Benign	0.88

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: rs3799703; hg19: chr6-38646630;