rs6932648

Positions:

• chr6-38691107-C-T

Variant summary

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

The ENST00000373365.5(GLO1):​c.85-4133G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.179 in 152,042 control chromosomes in the GnomAD database, including 3,036 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 (3036 hom., cov: 32)
• Consequence: GLO1 ENST00000373365.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0380

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.293 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GLO1	NM_006708.3	c.85-4133G>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.85-4133G>A		intron_variant		1	NM_006708.3	ENSP00000362463	P1

Frequencies

GnomAD3 genomes AF: 0.179 AC: 27192 AN: 151924 Hom.: 3033 Cov.: 32

Gnomad AFR AF: 0.297

Gnomad AMI AF: 0.0989

Gnomad AMR AF: 0.162

Gnomad ASJ AF: 0.235

Gnomad EAS AF: 0.232

Gnomad SAS AF: 0.242

Gnomad FIN AF: 0.0892

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.115

Gnomad OTH AF: 0.168

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

GnomAD4 genome AF: 0.179 AC: 27216 AN: 152042 Hom.: 3036 Cov.: 32 AF XY: 0.180 AC XY: 13395 AN XY: 74314

Gnomad4 AFR AF: 0.297

Gnomad4 AMR AF: 0.162

Gnomad4 ASJ AF: 0.235

Gnomad4 EAS AF: 0.232

Gnomad4 SAS AF: 0.241

Gnomad4 FIN AF: 0.0892

Gnomad4 NFE AF: 0.115

Gnomad4 OTH AF: 0.167

Alfa AF: 0.132 Hom.: 2322

Bravo AF: 0.187

Asia WGS AF: 0.217 AC: 751 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.3
DANN	Benign	0.70

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: rs6932648; hg19: chr6-38658883; COSMIC: COSV64905068;