16-70040823-G-A

Variant names:

• chr16-70040823-G-A
• rs2903718
• ENST00000531894.5:n.333+1528C>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000531894.5(PDXDC2P-NPIPB14P):​n.333+1528C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. 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-NPIPB14P ENST00000531894.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.66
• 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000531894.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PDXDC2P-NPIPB14P	NR_003610.1		n.333+1528C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PDXDC2P-NPIPB14P	ENST00000531894.5	TSL:1	n.333+1528C>T		intron	N/A
	PDXDC2P-NPIPB14P	ENST00000529089.1	TSL:2	n.203+1528C>T		intron	N/A
	PDXDC2P-NPIPB14P	ENST00000530079.5	TSL:5	n.238+1528C>T		intron	N/A

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

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.0000227

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	16
DANN	Benign	0.75
PhyloP100		1.7
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs2903718; hg19: chr16-70074726;