16-15031584-T-G

Position:

• chr16-15031584-T-G

Variant summary

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

The NM_015027.4(PDXDC1):​c.1400-151T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.323 in 603,230 control chromosomes in the GnomAD database, including 33,225 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 0.30 (7456 hom., cov: 31)
  • Exomes 𝑓: 0.33 (25769 hom.)
• Consequence: PDXDC1 NM_015027.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0400

Genes affected

PDXDC1 (HGNC:28995): (pyridoxal dependent decarboxylase domain containing 1) Enables cadherin binding activity. Predicted to be involved in carboxylic acid metabolic process. Located in Golgi apparatus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.433 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PDXDC1	NM_015027.4	c.1400-151T>G		intron_variant		ENST00000396410.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PDXDC1	ENST00000396410.9	c.1400-151T>G		intron_variant		1	NM_015027.4	P1

Frequencies

GnomAD3 genomes AF: 0.302 AC: 45825 AN: 151858 Hom.: 7434 Cov.: 31

Gnomad AFR AF: 0.210

Gnomad AMI AF: 0.246

Gnomad AMR AF: 0.442

Gnomad ASJ AF: 0.323

Gnomad EAS AF: 0.411

Gnomad SAS AF: 0.403

Gnomad FIN AF: 0.340

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.304

Gnomad OTH AF: 0.313

GnomAD4 exome AF: 0.329 AC: 148668 AN: 451254 Hom.: 25769 AF XY: 0.332 AC XY: 78238 AN XY: 235860

Gnomad4 AFR exome AF: 0.217

Gnomad4 AMR exome AF: 0.492

Gnomad4 ASJ exome AF: 0.322

Gnomad4 EAS exome AF: 0.473

Gnomad4 SAS exome AF: 0.381

Gnomad4 FIN exome AF: 0.319

Gnomad4 NFE exome AF: 0.301

Gnomad4 OTH exome AF: 0.324

GnomAD4 genome AF: 0.302 AC: 45893 AN: 151976 Hom.: 7456 Cov.: 31 AF XY: 0.308 AC XY: 22895 AN XY: 74268

Gnomad4 AFR AF: 0.210

Gnomad4 AMR AF: 0.442

Gnomad4 ASJ AF: 0.323

Gnomad4 EAS AF: 0.413

Gnomad4 SAS AF: 0.404

Gnomad4 FIN AF: 0.340

Gnomad4 NFE AF: 0.304

Gnomad4 OTH AF: 0.319

Alfa AF: 0.310 Hom.: 3816

Bravo AF: 0.308

Asia WGS AF: 0.442 AC: 1536 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.9
DANN	Benign	0.69

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs4985124; hg19: chr16-15125441;