chrX-30702378-A-G

Position:

• chrX-30702378-A-G

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The NM_001205019.2(GK):​c.851+1473A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.67 (17525 hom., 22382 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: GK NM_001205019.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.139

Genes affected

GK (HGNC:4289): (glycerol kinase) The protein encoded by this gene belongs to the FGGY kinase family. This protein is a key enzyme in the regulation of glycerol uptake and metabolism. It catalyzes the phosphorylation of glycerol by ATP, yielding ADP and glycerol-3-phosphate. Mutations in this gene are associated with glycerol kinase deficiency (GKD). Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Mar 2011]

GK-AS1 (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GK	NM_001205019.2	c.851+1473A>G		intron_variant		ENST00000427190.6	NP_001191948.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GK	ENST00000427190.6	c.851+1473A>G		intron_variant		5	NM_001205019.2	ENSP00000401720.2

Frequencies

GnomAD3 genomes AF: 0.670 AC: 74488 AN: 111219 Hom.: 17536 Cov.: 23 AF XY: 0.668 AC XY: 22345 AN XY: 33455

Gnomad AFR AF: 0.627

Gnomad AMI AF: 0.612

Gnomad AMR AF: 0.615

Gnomad ASJ AF: 0.632

Gnomad EAS AF: 0.771

Gnomad SAS AF: 0.847

Gnomad FIN AF: 0.725

Gnomad MID AF: 0.723

Gnomad NFE AF: 0.686

Gnomad OTH AF: 0.661

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

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.670 AC: 74505 AN: 111275 Hom.: 17525 Cov.: 23 AF XY: 0.668 AC XY: 22382 AN XY: 33521

Gnomad4 AFR AF: 0.626

Gnomad4 AMR AF: 0.616

Gnomad4 ASJ AF: 0.632

Gnomad4 EAS AF: 0.771

Gnomad4 SAS AF: 0.845

Gnomad4 FIN AF: 0.725

Gnomad4 NFE AF: 0.686

Gnomad4 OTH AF: 0.664

Alfa AF: 0.569 Hom.: 3502

Bravo AF: 0.659

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.91
DANN	Benign	0.51

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: rs6526997; hg19: chrX-30720495;