16-70034584-T-C

Variant summary

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

The NR_003610.1(PDXDC2P-NPIPB14P):n.562-224A>G 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 0.436 in 151,786 control chromosomes in the GnomAD database, including 15,058 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 0.44 (15058 hom., cov: 31)
• Consequence: PDXDC2P-NPIPB14P NR_003610.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17

Genes affected

PDXDC2P (HGNC:27559): (pyridoxal dependent decarboxylase domain containing 2, pseudogene) Predicted to enable carboxy-lyase activity and pyridoxal phosphate binding activity. Predicted to be involved in carboxylic acid metabolic process. Predicted to be active in intracellular membrane-bounded organelle. [provided by Alliance of Genome Resources, Apr 2022]

PDXDC2P-NPIPB14P (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.852 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PDXDC2P-NPIPB14P	NR_003610.1	n.562-224A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PDXDC2P	ENST00000534700.6	n.390-224A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.437 AC: 66215 AN: 151668 Hom.: 15056 Cov.: 31

Gnomad AFR AF: 0.445

Gnomad AMI AF: 0.390

Gnomad AMR AF: 0.450

Gnomad ASJ AF: 0.381

Gnomad EAS AF: 0.874

Gnomad SAS AF: 0.578

Gnomad FIN AF: 0.372

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.398

Gnomad OTH AF: 0.459

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

GnomAD4 genome AF: 0.436 AC: 66254 AN: 151786 Hom.: 15058 Cov.: 31 AF XY: 0.444 AC XY: 32947 AN XY: 74192

Gnomad4 AFR AF: 0.444

Gnomad4 AMR AF: 0.450

Gnomad4 ASJ AF: 0.381

Gnomad4 EAS AF: 0.873

Gnomad4 SAS AF: 0.579

Gnomad4 FIN AF: 0.372

Gnomad4 NFE AF: 0.398

Gnomad4 OTH AF: 0.462

Alfa AF: 0.400 Hom.: 1488

Bravo AF: 0.441

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	1.3
Dann	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2287968; hg19: chr16-70068487;