X-30667920-A-C

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_001205019.2(GK):​c.153-92A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00816 in 553,588 control chromosomes in the GnomAD database, including 140 homozygotes. There are 1,155 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.026 ( 98 hom., 753 hem., cov: 24)
Exomes 𝑓: 0.0036 ( 42 hom. 402 hem. )

Consequence

GK
NM_001205019.2 intron

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.339
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 -14 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BP6
Variant X-30667920-A-C is Benign according to our data. Variant chrX-30667920-A-C is described in ClinVar as [Benign]. Clinvar id is 1286744.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0867 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
GKNM_001205019.2 linkc.153-92A>C intron_variant Intron 2 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.153-92A>C intron_variant Intron 2 of 20 5 NM_001205019.2 ENSP00000401720.2 P32189-3

Frequencies

GnomAD3 genomes
AF:
0.0260
AC:
2911
AN:
112047
Hom.:
99
Cov.:
24
AF XY:
0.0220
AC XY:
752
AN XY:
34257
show subpopulations
Gnomad AFR
AF:
0.0896
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00942
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000620
Gnomad OTH
AF:
0.0153
GnomAD4 exome
AF:
0.00364
AC:
1607
AN:
441491
Hom.:
42
AF XY:
0.00263
AC XY:
402
AN XY:
152931
show subpopulations
Gnomad4 AFR exome
AF:
0.0882
Gnomad4 AMR exome
AF:
0.00567
Gnomad4 ASJ exome
AF:
0.0000681
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.000389
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.000326
Gnomad4 OTH exome
AF:
0.00783
GnomAD4 genome
AF:
0.0260
AC:
2912
AN:
112097
Hom.:
98
Cov.:
24
AF XY:
0.0219
AC XY:
753
AN XY:
34317
show subpopulations
Gnomad4 AFR
AF:
0.0895
Gnomad4 AMR
AF:
0.00932
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000620
Gnomad4 OTH
AF:
0.0151
Alfa
AF:
0.0302
Hom.:
82
Bravo
AF:
0.0304

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
May 21, 2021
GeneDx
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

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Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.85
CADD
Benign
1.0
DANN
Benign
0.41

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: rs45540243; hg19: chrX-30686037; COSMIC: COSV66734696; COSMIC: COSV66734696; API