X-30702378-A-G

Variant names:

• chrX-30702378-A-G
• rs6526997
• NM_001205019.2:c.851+1473A>G

Variant summary

Our verdict is Likely benign. The variant received -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
• Publications: 0 publications found

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:40255): (GK antisense RNA 1)

ENSG00000241886 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GK	NM_001205019.2	c.851+1473A>G		intron_variant	Intron 11 of 20	ENST00000427190.6	NP_001191948.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GK	ENST00000427190.6	c.851+1473A>G		intron_variant	Intron 11 of 20	5	NM_001205019.2	ENSP00000401720.2

Frequencies

GnomAD3 genomes AF: 0.670 AC: 74488 AN: 111219 Hom.: 17536 Cov.: 23

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

African (AFR) AF: 0.626 AC: 19161 AN: 30602

American (AMR) AF: 0.616 AC: 6471 AN: 10510

Ashkenazi Jewish (ASJ) AF: 0.632 AC: 1672 AN: 2645

East Asian (EAS) AF: 0.771 AC: 2737 AN: 3551

South Asian (SAS) AF: 0.845 AC: 2272 AN: 2688

European-Finnish (FIN) AF: 0.725 AC: 4253 AN: 5864

Middle Eastern (MID) AF: 0.724 AC: 155 AN: 214

European-Non Finnish (NFE) AF: 0.686 AC: 36366 AN: 53013

Other (OTH) AF: 0.664 AC: 1007 AN: 1516

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
PhyloP100		-0.14
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: rs6526997; hg19: chrX-30720495;