15-72790025-C-T

Variant names:

• chr15-72790025-C-T
• rs4777542
• ENST00000563592.5:n.2534+2432C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000563592.5(ADPGK-AS1):​n.2534+2432C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.43 in 152,062 control chromosomes in the GnomAD database, including 15,741 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 0.43 (15741 hom., cov: 33)
• Consequence: ADPGK-AS1 ENST00000563592.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13
• Publications: 8 publications found

Genes affected

ADPGK-AS1 (HGNC:44144): (ADPGK antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.729 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADPGK-AS1	NR_040107.1	n.2534+2432C>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADPGK-AS1	ENST00000563592.5	n.2534+2432C>T		intron_variant	Intron 2 of 2	2
ADPGK-AS1	ENST00000566745.1	n.357+2432C>T		intron_variant	Intron 2 of 2	3
ADPGK-AS1	ENST00000670622.2	n.419+2432C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.429 AC: 65232 AN: 151944 Hom.: 15715 Cov.: 33

Gnomad AFR AF: 0.611

Gnomad AMI AF: 0.222

Gnomad AMR AF: 0.437

Gnomad ASJ AF: 0.291

Gnomad EAS AF: 0.749

Gnomad SAS AF: 0.405

Gnomad FIN AF: 0.325

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.321

Gnomad OTH AF: 0.416

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.430 AC: 65326 AN: 152062 Hom.: 15741 Cov.: 33 AF XY: 0.430 AC XY: 31966 AN XY: 74316

African (AFR) AF: 0.611 AC: 25324 AN: 41446

American (AMR) AF: 0.438 AC: 6699 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.291 AC: 1007 AN: 3464

East Asian (EAS) AF: 0.748 AC: 3878 AN: 5182

South Asian (SAS) AF: 0.404 AC: 1952 AN: 4826

European-Finnish (FIN) AF: 0.325 AC: 3438 AN: 10566

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.321 AC: 21843 AN: 67978

Other (OTH) AF: 0.421 AC: 890 AN: 2114

Alfa AF: 0.410 Hom.: 8491

Bravo AF: 0.445

Asia WGS AF: 0.586 AC: 2032 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.61
DANN	Benign	0.40
PhyloP100		-1.1

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs4777542; hg19: chr15-73082366;