chrX-30653779-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBP6_Very_Strong

The NM_001205019.2(GK):​c.78+164G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.71 ( 20306 hom., 23786 hem., cov: 24)
Failed GnomAD Quality Control

Consequence

GK
NM_001205019.2 intron

Scores

2

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.173
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BP6
Variant X-30653779-G-C is Benign according to our data. Variant chrX-30653779-G-C is described in ClinVar as [Benign]. Clinvar id is 1281954.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
GKNM_001205019.2 linkc.78+164G>C intron_variant Intron 1 of 20 ENST00000427190.6 NP_001191948.1 P32189-3B4DH54

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
GKENST00000427190.6 linkc.78+164G>C intron_variant Intron 1 of 20 5 NM_001205019.2 ENSP00000401720.2 P32189-3

Frequencies

GnomAD3 genomes
AF:
0.711
AC:
79239
AN:
111377
Hom.:
20301
Cov.:
24
AF XY:
0.706
AC XY:
23720
AN XY:
33587
show subpopulations
Gnomad AFR
AF:
0.895
Gnomad AMI
AF:
0.539
Gnomad AMR
AF:
0.703
Gnomad ASJ
AF:
0.637
Gnomad EAS
AF:
0.647
Gnomad SAS
AF:
0.572
Gnomad FIN
AF:
0.677
Gnomad MID
AF:
0.530
Gnomad NFE
AF:
0.630
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:
0.712
AC:
79307
AN:
111431
Hom.:
20306
Cov.:
24
AF XY:
0.707
AC XY:
23786
AN XY:
33651
show subpopulations
Gnomad4 AFR
AF:
0.895
Gnomad4 AMR
AF:
0.704
Gnomad4 ASJ
AF:
0.637
Gnomad4 EAS
AF:
0.647
Gnomad4 SAS
AF:
0.572
Gnomad4 FIN
AF:
0.677
Gnomad4 NFE
AF:
0.630
Gnomad4 OTH
AF:
0.658
Alfa
AF:
0.691
Hom.:
5577
Bravo
AF:
0.721

ClinVar

Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not provided Benign:2
May 12, 2021
GeneDx
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

-
Breakthrough Genomics, Breakthrough Genomics
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: not provided

- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.82
CADD
Benign
7.3
DANN
Benign
0.29

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.

Other links and lift over

dbSNP: rs12854653; hg19: chrX-30671896; API