chr16-15035602-A-G

Position:

• chr16-15035602-A-G

Variant summary

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

The ENST00000396410.9(PDXDC1):​c.2107+49A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.36 in 1,108,538 control chromosomes in the GnomAD database, including 74,727 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 0.37 (10768 hom., cov: 32)
  • Exomes 𝑓: 0.36 (63959 hom.)
• Consequence: PDXDC1 ENST00000396410.9 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0490

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=-0.81).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.519 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PDXDC1	NM_015027.4	c.2107+49A>G		intron_variant		ENST00000396410.9	NP_055842.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PDXDC1	ENST00000396410.9	c.2107+49A>G		intron_variant		1	NM_015027.4	ENSP00000379691	P1

Frequencies

GnomAD3 genomes AF: 0.368 AC: 55946 AN: 151984 Hom.: 10726 Cov.: 32

Gnomad AFR AF: 0.340

Gnomad AMI AF: 0.294

Gnomad AMR AF: 0.528

Gnomad ASJ AF: 0.383

Gnomad EAS AF: 0.458

Gnomad SAS AF: 0.425

Gnomad FIN AF: 0.359

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.341

Gnomad OTH AF: 0.373

GnomAD3 exomes AF: 0.402 AC: 52731 AN: 131308 Hom.: 11180 AF XY: 0.396 AC XY: 27873 AN XY: 70420

Gnomad AFR exome AF: 0.346

Gnomad AMR exome AF: 0.623

Gnomad ASJ exome AF: 0.386

Gnomad EAS exome AF: 0.474

Gnomad SAS exome AF: 0.411

Gnomad FIN exome AF: 0.367

Gnomad NFE exome AF: 0.344

Gnomad OTH exome AF: 0.382

GnomAD4 exome AF: 0.358 AC: 342691 AN: 956436 Hom.: 63959 Cov.: 12 AF XY: 0.359 AC XY: 174134 AN XY: 485364

Gnomad4 AFR exome AF: 0.339

Gnomad4 AMR exome AF: 0.607

Gnomad4 ASJ exome AF: 0.384

Gnomad4 EAS exome AF: 0.524

Gnomad4 SAS exome AF: 0.406

Gnomad4 FIN exome AF: 0.349

Gnomad4 NFE exome AF: 0.337

Gnomad4 OTH exome AF: 0.368

GnomAD4 genome AF: 0.369 AC: 56050 AN: 152102 Hom.: 10768 Cov.: 32 AF XY: 0.374 AC XY: 27792 AN XY: 74364

Gnomad4 AFR AF: 0.340

Gnomad4 AMR AF: 0.528

Gnomad4 ASJ AF: 0.383

Gnomad4 EAS AF: 0.459

Gnomad4 SAS AF: 0.426

Gnomad4 FIN AF: 0.359

Gnomad4 NFE AF: 0.341

Gnomad4 OTH AF: 0.378

Alfa AF: 0.352 Hom.: 5873

Bravo AF: 0.383

Asia WGS AF: 0.465 AC: 1616 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	2.4
DANN	Benign	0.76
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: rs4985155; hg19: chr16-15129459;