15-72752234-G-A

Variant names:

• chr15-72752234-G-A
• rs9460
• ENST00000562621.1:n.3714C>T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000562621.1(ADPGK):​n.3714C>T variant causes a non coding transcript exon 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 ENST00000562621.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.02
• Publications: 20 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
ADPGK	NM_001365225.1	c.*107C>T		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	c.*107C>T		3_prime_UTR_variant	Exon 7 of 7	1	NM_001365225.1	ENSP00000397694.3

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

African (AFR) AF: 0.357 AC: 8092 AN: 22680

American (AMR) AF: 0.507 AC: 10471 AN: 20640

Ashkenazi Jewish (ASJ) AF: 0.675 AC: 11751 AN: 17406

East Asian (EAS) AF: 0.224 AC: 7577 AN: 33856

South Asian (SAS) AF: 0.595 AC: 33936 AN: 57002

European-Finnish (FIN) AF: 0.660 AC: 23839 AN: 36098

Middle Eastern (MID) AF: 0.654 AC: 2054 AN: 3142

European-Non Finnish (NFE) AF: 0.640 AC: 496626 AN: 776438

Other (OTH) AF: 0.588 AC: 26096 AN: 44374

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

African (AFR) AF: 0.361 AC: 14969 AN: 41476

American (AMR) AF: 0.532 AC: 8143 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.672 AC: 2331 AN: 3468

East Asian (EAS) AF: 0.244 AC: 1262 AN: 5178

South Asian (SAS) AF: 0.578 AC: 2787 AN: 4822

European-Finnish (FIN) AF: 0.657 AC: 6966 AN: 10604

Middle Eastern (MID) AF: 0.687 AC: 202 AN: 294

European-Non Finnish (NFE) AF: 0.641 AC: 43570 AN: 67986

Other (OTH) AF: 0.560 AC: 1182 AN: 2110

Alfa AF: 0.603 Hom.: 83644

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
PhyloP100		4.0
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

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