dbSNP rs6584202: PYROXD2:c.147+313C>T (chr10-98410626-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_032709.3(PYROXD2):c.147+313C>T 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 430,030 control chromosomes in the GnomAD database, including 26,272 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 0.38 ( 12669 hom., cov: 32)

Exomes 𝑓: 0.29 ( 13603 hom. )

Consequence

PYROXD2
NM_032709.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.855

Publications

20 publications found

Variant links:

Genes affected

PYROXD2 (HGNC:23517): (pyridine nucleotide-disulphide oxidoreductase domain 2) Predicted to enable oxidoreductase activity. Involved in mitochondrion organization. Located in mitochondrial matrix. [provided by Alliance of Genome Resources, Apr 2022]

PYROXD2 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 (AFR) allele frequency at 95% confidence interval = 0.589 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_032709.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PYROXD2	NM_032709.3	MANE Select	c.147+313C>T		intron	N/A	NP_116098.2	Q8N2H3

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
PYROXD2	ENST00000370575.5	TSL:1 MANE Select	c.147+313C>T	intron	N/A	ENSP00000359607.4	Q8N2H3
PYROXD2	ENST00000483923.5	TSL:1	n.1036C>T	non_coding_transcript_exon	Exon 2 of 15
PYROXD2	ENST00000906254.1		c.147+313C>T	intron	N/A	ENSP00000576313.1

Frequencies

GnomAD3 genomes

AF:

0.381

AC:

57821

AN:

151888

Hom.:

12644

Cov.:

show subpopulations

Gnomad AFR

AF:

0.595

Gnomad AMI

AF:

0.272

Gnomad AMR

AF:

0.391

Gnomad ASJ

AF:

0.354

Gnomad EAS

AF:

0.440

Gnomad SAS

AF:

0.487

Gnomad FIN

AF:

0.236

Gnomad MID

AF:

0.354

Gnomad NFE

AF:

0.262

Gnomad OTH

AF:

0.353

GnomAD4 exome

AF:

0.292

AC:

81204

AN:

278024

Hom.:

13603

Cov.:

AF XY:

0.298

AC XY:

42815

AN XY:

143856

show subpopulations

African (AFR)

AF:

0.585

AC:

4551

AN:

7778

American (AMR)

AF:

0.376

AC:

3659

AN:

9732

Ashkenazi Jewish (ASJ)

AF:

0.326

AC:

3096

AN:

9484

East Asian (EAS)

AF:

0.386

AC:

7208

AN:

18696

South Asian (SAS)

AF:

0.470

AC:

10133

AN:

21540

European-Finnish (FIN)

AF:

0.212

AC:

4082

AN:

19276

Middle Eastern (MID)

AF:

0.360

AC:

502

AN:

1394

European-Non Finnish (NFE)

AF:

0.246

AC:

42520

AN:

172866

Other (OTH)

AF:

0.316

AC:

5453

AN:

17258

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.495

Heterozygous variant carriers

2564

5127

7691

10254

12818

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

312

624

936

1248

1560

<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:

0.381

AC:

57895

AN:

152006

Hom.:

12669

Cov.:

AF XY:

0.382

AC XY:

28401

AN XY:

74298

show subpopulations

African (AFR)

AF:

0.595

AC:

24681

AN:

41450

American (AMR)

AF:

0.391

AC:

5981

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.354

AC:

1229

AN:

3470

East Asian (EAS)

AF:

0.439

AC:

2263

AN:

5150

South Asian (SAS)

AF:

0.486

AC:

2340

AN:

4816

European-Finnish (FIN)

AF:

0.236

AC:

2491

AN:

10568

Middle Eastern (MID)

AF:

0.354

AC:

104

AN:

294

European-Non Finnish (NFE)

AF:

0.262

AC:

17816

AN:

67944

Other (OTH)

AF:

0.352

AC:

742

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1685

3370

5054

6739

8424

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

552

1104

1656

2208

2760

<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:

0.329

Hom.:

15769

Bravo

AF:

0.396

Asia WGS

AF:

0.466

AC:

1618

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

0.051

(source)

DANN

Benign

0.33

PhyloP100

-0.85

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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