chr16-70034584-T-C

Variant names:

• chr16-70034584-T-C
• rs2287968
• ENST00000531894.5:n.562-224A>G

Variant summary

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

The ENST00000531894.5(PDXDC2P-NPIPB14P):​n.562-224A>G variant causes a intron 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 ENST00000531894.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17
• Publications: 1 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
PDXDC2P		n.70034584T>C		intragenic_variant
PDXDC2P-NPIPB14P	NR_003610.1	n.562-224A>G		intron_variant	Intron 5 of 25

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PDXDC2P-NPIPB14P	ENST00000531894.5	n.562-224A>G		intron_variant	Intron 5 of 25	1
PDXDC2P-NPIPB14P	ENST00000529089.1	n.432-224A>G		intron_variant	Intron 5 of 17	2
PDXDC2P-NPIPB14P	ENST00000530079.5	n.582-224A>G		intron_variant	Intron 5 of 24	5
PDXDC2P	ENST00000534700.6	n.390-224A>G		intron_variant	Intron 5 of 15	6

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

African (AFR) AF: 0.444 AC: 18377 AN: 41376

American (AMR) AF: 0.450 AC: 6869 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.381 AC: 1320 AN: 3468

East Asian (EAS) AF: 0.873 AC: 4518 AN: 5174

South Asian (SAS) AF: 0.579 AC: 2786 AN: 4814

European-Finnish (FIN) AF: 0.372 AC: 3902 AN: 10482

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.398 AC: 27023 AN: 67914

Other (OTH) AF: 0.462 AC: 972 AN: 2106

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
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs2287968; hg19: chr16-70068487;