6-38678854-A-G

Variant names:

• chr6-38678854-A-G
• rs3799703
• NM_006708.3:c.467-1471T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

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]

ENSG00000298390 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GLO1	NM_006708.3	MANE Select	c.467-1471T>C		intron	N/A	NP_006699.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GLO1	ENST00000373365.5	TSL:1 MANE Select	c.467-1471T>C		intron	N/A	ENSP00000362463.3
	GLO1	ENST00000470973.1	TSL:2	n.499-1471T>C		intron	N/A
	ENSG00000298390	ENST00000755274.1		n.480+24187A>G		intron	N/A

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

African (AFR) AF: 0.462 AC: 19084 AN: 41316

American (AMR) AF: 0.475 AC: 7223 AN: 15208

Ashkenazi Jewish (ASJ) AF: 0.536 AC: 1858 AN: 3468

East Asian (EAS) AF: 0.276 AC: 1423 AN: 5154

South Asian (SAS) AF: 0.416 AC: 1993 AN: 4794

European-Finnish (FIN) AF: 0.417 AC: 4411 AN: 10570

Middle Eastern (MID) AF: 0.497 AC: 146 AN: 294

European-Non Finnish (NFE) AF: 0.536 AC: 36427 AN: 67904

Other (OTH) AF: 0.455 AC: 960 AN: 2110

Alfa AF: 0.509 Hom.: 13373

Bravo AF: 0.484

Asia WGS AF: 0.337 AC: 1172 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.2
DANN	Benign	0.88
PhyloP100		-0.047
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs3799703; hg19: chr6-38646630;