Genetic Variant PDXDC1:c.1400-151T>G (chr16-15031584-T-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0400

Publications

20 publications found

Variant links:

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]

PDXDC1 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015027.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
PDXDC1	NM_015027.4	MANE Select	c.1400-151T>G	intron	N/A	NP_055842.2
PDXDC1	NM_001324019.2		c.1397-151T>G	intron	N/A	NP_001310948.1
PDXDC1	NM_001285447.1		c.1355-151T>G	intron	N/A	NP_001272376.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
PDXDC1	ENST00000396410.9	TSL:1 MANE Select	c.1400-151T>G	intron	N/A	ENSP00000379691.4
PDXDC1	ENST00000569715.5	TSL:1	c.1319-151T>G	intron	N/A	ENSP00000455070.1
PDXDC1	ENST00000535621.6	TSL:1	c.1399+1528T>G	intron	N/A	ENSP00000437835.2

Frequencies

GnomAD3 genomes

AF:

0.302

AC:

45825

AN:

151858

Hom.:

7434

Cov.:

show subpopulations

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

show subpopulations

African (AFR)

AF:

0.217

AC:

2787

AN:

12826

American (AMR)

AF:

0.492

AC:

9396

AN:

19088

Ashkenazi Jewish (ASJ)

AF:

0.322

AC:

4314

AN:

13384

East Asian (EAS)

AF:

0.473

AC:

14868

AN:

31438

South Asian (SAS)

AF:

0.381

AC:

15906

AN:

41794

European-Finnish (FIN)

AF:

0.319

AC:

11169

AN:

34982

Middle Eastern (MID)

AF:

0.270

AC:

510

AN:

1886

European-Non Finnish (NFE)

AF:

0.301

AC:

81413

AN:

270234

Other (OTH)

AF:

0.324

AC:

8305

AN:

25622

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

4995

9990

14985

19980

24975

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

684

1368

2052

2736

3420

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.302

AC:

45893

AN:

151976

Hom.:

7456

Cov.:

AF XY:

0.308

AC XY:

22895

AN XY:

74268

show subpopulations

African (AFR)

AF:

0.210

AC:

8702

AN:

41448

American (AMR)

AF:

0.442

AC:

6751

AN:

15266

Ashkenazi Jewish (ASJ)

AF:

0.323

AC:

1119

AN:

3468

East Asian (EAS)

AF:

0.413

AC:

2124

AN:

5148

South Asian (SAS)

AF:

0.404

AC:

1949

AN:

4824

European-Finnish (FIN)

AF:

0.340

AC:

3589

AN:

10558

Middle Eastern (MID)

AF:

0.252

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.304

AC:

20689

AN:

67952

Other (OTH)

AF:

0.319

AC:

672

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1591

3182

4773

6364

7955

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

466

932

1398

1864

2330

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.307

Hom.:

12695

Bravo

AF:

0.308

Asia WGS

AF:

0.442

AC:

1536

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

1.9

(source)

DANN

Benign

0.69

PhyloP100

-0.040

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over