6-38696818-C-T

Position:

• chr6-38696818-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.84+6153G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.183 in 152,110 control chromosomes in the GnomAD database, including 3,209 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 0.18 (3209 hom., cov: 32)
• Consequence: GLO1 NM_006708.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0730

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=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.267 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GLO1	NM_006708.3	c.84+6153G>A		intron_variant		ENST00000373365.5	NP_006699.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GLO1	ENST00000373365.5	c.84+6153G>A		intron_variant		1	NM_006708.3	ENSP00000362463.3

Frequencies

GnomAD3 genomes AF: 0.183 AC: 27764 AN: 151996 Hom.: 3208 Cov.: 32

Gnomad AFR AF: 0.0550

Gnomad AMI AF: 0.444

Gnomad AMR AF: 0.184

Gnomad ASJ AF: 0.184

Gnomad EAS AF: 0.0397

Gnomad SAS AF: 0.113

Gnomad FIN AF: 0.200

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.270

Gnomad OTH AF: 0.174

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

GnomAD4 genome AF: 0.183 AC: 27764 AN: 152110 Hom.: 3209 Cov.: 32 AF XY: 0.176 AC XY: 13121 AN XY: 74362

Gnomad4 AFR AF: 0.0550

Gnomad4 AMR AF: 0.183

Gnomad4 ASJ AF: 0.184

Gnomad4 EAS AF: 0.0398

Gnomad4 SAS AF: 0.114

Gnomad4 FIN AF: 0.200

Gnomad4 NFE AF: 0.270

Gnomad4 OTH AF: 0.173

Alfa AF: 0.245 Hom.: 6428

Bravo AF: 0.173

Asia WGS AF: 0.0800 AC: 280 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.72
DANN	Benign	0.47

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: rs10484854; hg19: chr6-38664594;