Genetic Variant ADPGK:n.3714C>G (chr15-72752234-G-C) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The ENST00000562621.1(ADPGK):n.3714C>G variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.000000986 in 1,013,832 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 33)

Exomes 𝑓: 9.9e-7 ( 0 hom. )

Consequence

ADPGK
ENST00000562621.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 4.02

Publications

20 publications found

Variant links:

Genes affected

ADPGK (HGNC:25250): (ADP dependent glucokinase) ADPGK (EC 2.7.1.147) catalyzes the ADP-dependent phosphorylation of glucose to glucose-6-phosphate and may play a role in glycolysis, possibly during ischemic conditions (Ronimus and Morgan, 2004 [PubMed 14975750]).[supplied by OMIM, Mar 2008]

ADPGK links:

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.5).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADPGK	NM_001365225.1 link	c.*107C>G		3_prime_UTR_variant	Exon 7 of 7	ENST00000456471.3	NP_001352154.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADPGK	ENST00000456471.3 link	c.*107C>G		3_prime_UTR_variant	Exon 7 of 7	1	NM_001365225.1	ENSP00000397694.3		Q9BRR6-1

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

9.86e-7

AC:

AN:

1013832

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

502556

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

22726

American (AMR)

AF:

0.00

AC:

AN:

20658

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

17414

East Asian (EAS)

AF:

0.00

AC:

AN:

33870

South Asian (SAS)

AF:

0.00

AC:

AN:

57106

European-Finnish (FIN)

AF:

0.00

AC:

AN:

36126

Middle Eastern (MID)

AF:

0.00

AC:

AN:

3144

European-Non Finnish (NFE)

AF:

0.00000128

AC:

AN:

778330

Other (OTH)

AF:

0.00

AC:

AN:

44458

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.475

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

Cov.:

Alfa

AF:

0.00

Hom.:

83644

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.50

CADD

Benign

(source)

DANN

Benign

0.89

PhyloP100

4.0

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over