15-72790025-C-T

Position:

• chr15-72790025-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_040107.1(ADPGK-AS1):​n.2534+2432C>T variant causes a intron, non coding transcript 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 NR_040107.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
ADPGK-AS1	NR_040107.1	n.2534+2432C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ADPGK-AS1	ENST00000563592.5	n.2534+2432C>T		intron_variant, non_coding_transcript_variant		2
ADPGK-AS1	ENST00000566745.1	n.357+2432C>T		intron_variant, non_coding_transcript_variant		3
ADPGK-AS1	ENST00000670622.1	n.239+2432C>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.611

Gnomad4 AMR AF: 0.438

Gnomad4 ASJ AF: 0.291

Gnomad4 EAS AF: 0.748

Gnomad4 SAS AF: 0.404

Gnomad4 FIN AF: 0.325

Gnomad4 NFE AF: 0.321

Gnomad4 OTH AF: 0.421

Alfa AF: 0.276 Hom.: 1214

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4777542; hg19: chr15-73082366;