Variant X-30670598-ATT-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_001205019.2(GK):c.259+2490_259+2491delTT variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.20 ( 1646 hom., 5796 hem., cov: 16)

Consequence

GK
NM_001205019.2 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.149

Variant links:

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 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant X-30670598-ATT-A is Benign according to our data. Variant chrX-30670598-ATT-A is described in ClinVar as [Benign]. Clinvar id is 1235625.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.264 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GK	NM_001205019.2 link	c.259+2490_259+2491delTT		intron_variant	Intron 3 of 20	ENST00000427190.6	NP_001191948.1	P32189-3B4DH54

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GK	ENST00000427190.6 link	c.259+2481_259+2482delTT		intron_variant	Intron 3 of 20	5	NM_001205019.2	ENSP00000401720.2		P32189-3

Frequencies

GnomAD3 genomes

AF:

0.195

AC:

20735

AN:

106175

Hom.:

1650

Cov.:

AF XY:

0.194

AC XY:

5790

AN XY:

29901

show subpopulations

Gnomad AFR

AF:

0.0977

Gnomad AMI

AF:

0.313

Gnomad AMR

AF:

0.273

Gnomad ASJ

AF:

0.260

Gnomad EAS

AF:

0.227

Gnomad SAS

AF:

0.114

Gnomad FIN

AF:

0.208

Gnomad MID

AF:

0.205

Gnomad NFE

AF:

0.232

Gnomad OTH

AF:

0.196

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

GnomAD4 genome

AF:

0.195

AC:

20738

AN:

106195

Hom.:

1646

Cov.:

AF XY:

0.194

AC XY:

5796

AN XY:

29933

show subpopulations

Gnomad4 AFR

AF:

0.0977

Gnomad4 AMR

AF:

0.273

Gnomad4 ASJ

AF:

0.260

Gnomad4 EAS

AF:

0.227

Gnomad4 SAS

AF:

0.115

Gnomad4 FIN

AF:

0.208

Gnomad4 NFE

AF:

0.232

Gnomad4 OTH

AF:

0.195

Alfa

AF:

0.0762

Hom.:

297

Bravo

AF:

0.200

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Jun 20, 2021

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over