Genetic Variant PDXDC1:c.2107+49A>G (chr16-15035602-A-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.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
NM_015027.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0490

Publications

72 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=-0.81).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.519 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.2107+49A>G	intron	N/A	NP_055842.2
PDXDC1	NM_001324019.2		c.2104+49A>G	intron	N/A	NP_001310948.1
PDXDC1	NM_001285447.1		c.2062+49A>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.2107+49A>G	intron	N/A	ENSP00000379691.4
PDXDC1	ENST00000569715.5	TSL:1	c.2026+49A>G	intron	N/A	ENSP00000455070.1
PDXDC1	ENST00000535621.6	TSL:1	c.1399+5546A>G	intron	N/A	ENSP00000437835.2

Frequencies

GnomAD3 genomes

AF:

0.368

AC:

55946

AN:

151984

Hom.:

10726

Cov.:

show subpopulations

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

GnomAD2 exomes

AF:

0.402

AC:

52731

AN:

131308

AF XY:

0.396

show subpopulations

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 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.:

AF XY:

0.359

AC XY:

174134

AN XY:

485364

show subpopulations

African (AFR)

AF:

0.339

AC:

7425

AN:

21900

American (AMR)

AF:

0.607

AC:

15204

AN:

25036

Ashkenazi Jewish (ASJ)

AF:

0.384

AC:

7505

AN:

19558

East Asian (EAS)

AF:

0.524

AC:

17670

AN:

33744

South Asian (SAS)

AF:

0.406

AC:

26318

AN:

64754

European-Finnish (FIN)

AF:

0.349

AC:

16993

AN:

48674

Middle Eastern (MID)

AF:

0.339

AC:

1174

AN:

3464

European-Non Finnish (NFE)

AF:

0.337

AC:

234608

AN:

696414

Other (OTH)

AF:

0.368

AC:

15794

AN:

42892

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

10665

21330

31995

42660

53325

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

6550

13100

19650

26200

32750

<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:

0.369

AC:

56050

AN:

152102

Hom.:

10768

Cov.:

AF XY:

0.374

AC XY:

27792

AN XY:

74364

show subpopulations

African (AFR)

AF:

0.340

AC:

14125

AN:

41508

American (AMR)

AF:

0.528

AC:

8081

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.383

AC:

1330

AN:

3470

East Asian (EAS)

AF:

0.459

AC:

2364

AN:

5152

South Asian (SAS)

AF:

0.426

AC:

2053

AN:

4822

European-Finnish (FIN)

AF:

0.359

AC:

3792

AN:

10576

Middle Eastern (MID)

AF:

0.327

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.341

AC:

23143

AN:

67964

Other (OTH)

AF:

0.378

AC:

798

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1801

3601

5402

7202

9003

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

542

1084

1626

2168

2710

<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:

0.357

Hom.:

21706

Bravo

AF:

0.383

Asia WGS

AF:

0.465

AC:

1616

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

2.4

(source)

DANN

Benign

0.76

PhyloP100

-0.049

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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