rs9460

chr15-72752234-G-Achr15-72752234-G-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_001365225.1(ADPGK):c.*107C>T variant causes a 3 prime UTR change. The variant allele was found at a frequency of 0.604 in 1,163,778 control chromosomes in the GnomAD database, including 218,262 homozygotes. 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 0.54 (23712 hom., cov: 33)
  • Exomes 𝑓: 0.61 (194550 hom.)
• Consequence: ADPGK NM_001365225.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.02

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]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.46).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.636 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ADPGK	NM_001365225.1	c.*107C>T		3_prime_UTR_variant	7/7	ENST00000456471.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ADPGK	ENST00000456471.3	c.*107C>T		3_prime_UTR_variant	7/7	1	NM_001365225.1	P4

Frequencies

GnomAD3 genomes AF: 0.540 AC: 82046 AN: 152024 Hom.: 23730 Cov.: 33

Gnomad AFR AF: 0.361

Gnomad AMI AF: 0.698

Gnomad AMR AF: 0.533

Gnomad ASJ AF: 0.672

Gnomad EAS AF: 0.243

Gnomad SAS AF: 0.578

Gnomad FIN AF: 0.657

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.641

Gnomad OTH AF: 0.566

GnomAD4 exome AF: 0.613 AC: 620442 AN: 1011636 Hom.: 194550 Cov.: 13 AF XY: 0.615 AC XY: 308404 AN XY: 501494

Gnomad4 AFR exome AF: 0.357

Gnomad4 AMR exome AF: 0.507

Gnomad4 ASJ exome AF: 0.675

Gnomad4 EAS exome AF: 0.224

Gnomad4 SAS exome AF: 0.595

Gnomad4 FIN exome AF: 0.660

Gnomad4 NFE exome AF: 0.640

Gnomad4 OTH exome AF: 0.588

GnomAD4 genome AF: 0.539 AC: 82047 AN: 152142 Hom.: 23712 Cov.: 33 AF XY: 0.541 AC XY: 40282 AN XY: 74400

Gnomad4 AFR AF: 0.361

Gnomad4 AMR AF: 0.532

Gnomad4 ASJ AF: 0.672

Gnomad4 EAS AF: 0.244

Gnomad4 SAS AF: 0.578

Gnomad4 FIN AF: 0.657

Gnomad4 NFE AF: 0.641

Gnomad4 OTH AF: 0.560

Alfa AF: 0.619 Hom.: 51013

Bravo AF: 0.523

Asia WGS AF: 0.392 AC: 1369 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.46
Cadd	Benign	18
Dann	Benign	0.89

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

Other links and lift over

dbSNP: rs9460; hg19: chr15-73044575; COSMIC: COSV61174920; COSMIC: COSV61174920;