dbSNP rs7192563: PDXDC1:c.1813-157T>C (chr16-15034129-T-C) – 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.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
NM_015027.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.48

Publications

18 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:

Genome browser will be placed here

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=-0.9).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.859 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.1813-157T>C	intron	N/A	NP_055842.2
PDXDC1	NM_001324019.2		c.1810-157T>C	intron	N/A	NP_001310948.1
PDXDC1	NM_001285447.1		c.1768-157T>C	intron	N/A	NP_001272376.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
PDXDC1	ENST00000396410.9	TSL:1 MANE Select	c.1813-157T>C	intron	N/A	ENSP00000379691.4
PDXDC1	ENST00000569715.5	TSL:1	c.1732-157T>C	intron	N/A	ENSP00000455070.1
PDXDC1	ENST00000535621.6	TSL:1	c.1399+4073T>C	intron	N/A	ENSP00000437835.2

Frequencies

GnomAD3 genomes

AF:

0.783

AC:

119047

AN:

152014

Hom.:

47571

Cov.:

show subpopulations

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.:

AF XY:

0.828

AC XY:

210017

AN XY:

253662

show subpopulations

African (AFR)

AF:

0.614

AC:

8205

AN:

13362

American (AMR)

AF:

0.900

AC:

21288

AN:

23660

Ashkenazi Jewish (ASJ)

AF:

0.860

AC:

12861

AN:

14950

East Asian (EAS)

AF:

0.689

AC:

21569

AN:

31308

South Asian (SAS)

AF:

0.779

AC:

37780

AN:

48526

European-Finnish (FIN)

AF:

0.878

AC:

27133

AN:

30910

Middle Eastern (MID)

AF:

0.843

AC:

1714

AN:

2034

European-Non Finnish (NFE)

AF:

0.853

AC:

247385

AN:

290136

Other (OTH)

AF:

0.828

AC:

22563

AN:

27258

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

3606

7213

10819

14426

18032

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1246

2492

3738

4984

6230

<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:

0.783

AC:

119159

AN:

152132

Hom.:

47628

Cov.:

AF XY:

0.786

AC XY:

58437

AN XY:

74376

show subpopulations

African (AFR)

AF:

0.610

AC:

25303

AN:

41458

American (AMR)

AF:

0.872

AC:

13323

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.864

AC:

2997

AN:

3470

East Asian (EAS)

AF:

0.670

AC:

3458

AN:

5162

South Asian (SAS)

AF:

0.776

AC:

3735

AN:

4816

European-Finnish (FIN)

AF:

0.885

AC:

9384

AN:

10602

Middle Eastern (MID)

AF:

0.844

AC:

248

AN:

294

European-Non Finnish (NFE)

AF:

0.856

AC:

58201

AN:

68020

Other (OTH)

AF:

0.806

AC:

1705

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.511

Heterozygous variant carriers

1249

2498

3748

4997

6246

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

862

1724

2586

3448

4310

<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:

0.826

Hom.:

149668

Bravo

AF:

0.776

Asia WGS

AF:

0.752

AC:

2615

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.21

(source)

DANN

Benign

0.26

PhyloP100

-1.5

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