2-172550832-C-T

Variant summary

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

The ENST00000442417.5(PDK1-AS1):n.441+5257G>A 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 0.356 in 151,956 control chromosomes in the GnomAD database, including 12,055 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 0.36 (12055 hom., cov: 32)
• Consequence: PDK1-AS1 ENST00000442417.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.627

Genes affected

PDK1-AS1 (HGNC:40441): (PDK1 and ITGA6 antisense RNA 1)

LOC124900513 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.628 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124900513	XR_007087304.1	n.376+5257G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PDK1-AS1	ENST00000442417.5	n.441+5257G>A		intron_variant, non_coding_transcript_variant		3
PDK1-AS1	ENST00000450443.1	n.508+5257G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.355 AC: 53905 AN: 151838 Hom.: 12003 Cov.: 32

Gnomad AFR AF: 0.634

Gnomad AMI AF: 0.265

Gnomad AMR AF: 0.341

Gnomad ASJ AF: 0.260

Gnomad EAS AF: 0.322

Gnomad SAS AF: 0.363

Gnomad FIN AF: 0.198

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.223

Gnomad OTH AF: 0.310

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

GnomAD4 genome AF: 0.356 AC: 54029 AN: 151956 Hom.: 12055 Cov.: 32 AF XY: 0.354 AC XY: 26307 AN XY: 74268

Gnomad4 AFR AF: 0.635

Gnomad4 AMR AF: 0.341

Gnomad4 ASJ AF: 0.260

Gnomad4 EAS AF: 0.322

Gnomad4 SAS AF: 0.362

Gnomad4 FIN AF: 0.198

Gnomad4 NFE AF: 0.223

Gnomad4 OTH AF: 0.315

Alfa AF: 0.239 Hom.: 6325

Bravo AF: 0.380

Asia WGS AF: 0.378 AC: 1311 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	4.0
Dann	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12151618; hg19: chr2-173415560;