chr16-15034129-T-C

Position:

• chr16-15034129-T-C

Variant summary

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

The ENST00000396410.9(PDXDC1):​c.1813-157T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.819 in 634,276 control chromosomes in the GnomAD database, including 215,085 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 0.78 (47628 hom., cov: 33)
  • Exomes 𝑓: 0.83 (167457 hom.)
• Consequence: PDXDC1 ENST00000396410.9 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.48

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.859 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PDXDC1	NM_015027.4	c.1813-157T>C		intron_variant		ENST00000396410.9	NP_055842.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PDXDC1	ENST00000396410.9	c.1813-157T>C		intron_variant		1	NM_015027.4	ENSP00000379691	P1

Frequencies

GnomAD3 genomes AF: 0.783 AC: 119047 AN: 152014 Hom.: 47571 Cov.: 33

Gnomad AFR AF: 0.610

Gnomad AMI AF: 0.883

Gnomad AMR AF: 0.872

Gnomad ASJ AF: 0.864

Gnomad EAS AF: 0.669

Gnomad SAS AF: 0.775

Gnomad FIN AF: 0.885

Gnomad MID AF: 0.835

Gnomad NFE AF: 0.856

Gnomad OTH AF: 0.804

GnomAD4 exome AF: 0.831 AC: 400498 AN: 482144 Hom.: 167457 Cov.: 5 AF XY: 0.828 AC XY: 210017 AN XY: 253662

Gnomad4 AFR exome AF: 0.614

Gnomad4 AMR exome AF: 0.900

Gnomad4 ASJ exome AF: 0.860

Gnomad4 EAS exome AF: 0.689

Gnomad4 SAS exome AF: 0.779

Gnomad4 FIN exome AF: 0.878

Gnomad4 NFE exome AF: 0.853

Gnomad4 OTH exome AF: 0.828

GnomAD4 genome AF: 0.783 AC: 119159 AN: 152132 Hom.: 47628 Cov.: 33 AF XY: 0.786 AC XY: 58437 AN XY: 74376

Gnomad4 AFR AF: 0.610

Gnomad4 AMR AF: 0.872

Gnomad4 ASJ AF: 0.864

Gnomad4 EAS AF: 0.670

Gnomad4 SAS AF: 0.776

Gnomad4 FIN AF: 0.885

Gnomad4 NFE AF: 0.856

Gnomad4 OTH AF: 0.806

Alfa AF: 0.839 Hom.: 57116

Bravo AF: 0.776

Asia WGS AF: 0.752 AC: 2615 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.21
DANN	Benign	0.26
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs7192563; hg19: chr16-15127986;