rs1121

Positions:

• chr16-15037219-G-A
• chr16-15037219-G-T

Variant summary

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

The NM_015027.4(PDXDC1):​c.*944G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.302 in 152,046 control chromosomes in the GnomAD database, including 7,446 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 (7445 hom., cov: 32)
  • Exomes 𝑓: 0.38 (1 hom.)
• Consequence: PDXDC1 NM_015027.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.233

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=-0.84).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.431 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PDXDC1	NM_015027.4	c.*944G>A		3_prime_UTR_variant	23/23	ENST00000396410.9	NP_055842.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PDXDC1	ENST00000396410.9	c.*944G>A		3_prime_UTR_variant	23/23	1	NM_015027.4	ENSP00000379691.4

Frequencies

GnomAD3 genomes AF: 0.302 AC: 45853 AN: 151912 Hom.: 7423 Cov.: 32

Gnomad AFR AF: 0.215

Gnomad AMI AF: 0.246

Gnomad AMR AF: 0.440

Gnomad ASJ AF: 0.318

Gnomad EAS AF: 0.383

Gnomad SAS AF: 0.402

Gnomad FIN AF: 0.339

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.304

Gnomad OTH AF: 0.315

GnomAD4 exome AF: 0.375 AC: 6 AN: 16 Hom.: 1 Cov.: 0 AF XY: 0.200 AC XY: 2 AN XY: 10

Gnomad4 SAS exome AF: 0.500

Gnomad4 NFE exome AF: 0.357

GnomAD4 genome AF: 0.302 AC: 45922 AN: 152030 Hom.: 7445 Cov.: 32 AF XY: 0.308 AC XY: 22866 AN XY: 74306

Gnomad4 AFR AF: 0.216

Gnomad4 AMR AF: 0.440

Gnomad4 ASJ AF: 0.318

Gnomad4 EAS AF: 0.384

Gnomad4 SAS AF: 0.403

Gnomad4 FIN AF: 0.339

Gnomad4 NFE AF: 0.304

Gnomad4 OTH AF: 0.321

Alfa AF: 0.307 Hom.: 7315

Bravo AF: 0.309

Asia WGS AF: 0.425 AC: 1475 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	7.1
DANN	Benign	0.64
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: rs1121; hg19: chr16-15131076;