rs2868008

Variant names:

• chr16-70035137-A-G
• rs2868008
• ENST00000531894.5:n.562-777T>C

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• Consequence: PDXDC2P intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.493

Genes affected

PDXDC2P-NPIPB14P (HGNC:53158): (PDXDC2P-NPIPB14P readthrough, transcribed pseudogene) This locus represents naturally-occurring readthrough transcription between two pseudogenes, PDXDC2P (pyridoxal dependent decarboxylase domain containing 2, pseudogene) and NPIPB14P (nuclear pore complex interacting protein family, member B14, pseudogene). The individual pseudogene loci are not curated as transcribed regions. Readthrough transcripts likely do not encode functional proteins. [provided by RefSeq, Feb 2017]

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]

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PDXDC2P		n.70035137A>G		intragenic_variant
PDXDC2P-NPIPB14P	NR_003610.1	n.562-777T>C		intron_variant	Intron 5 of 25

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PDXDC2P-NPIPB14P	ENST00000531894.5	n.562-777T>C		intron_variant	Intron 5 of 25	1
PDXDC2P-NPIPB14P	ENST00000529089.1	n.432-777T>C		intron_variant	Intron 5 of 17	2
PDXDC2P-NPIPB14P	ENST00000530079.5	n.582-777T>C		intron_variant	Intron 5 of 24	5
PDXDC2P	ENST00000534700.6	n.390-777T>C		intron_variant	Intron 5 of 15	6

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.97
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2868008; hg19: chr16-70069040;