Genetic Variant PYROXD2:n.1036C>G (chr10-98410626-G-C) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The ENST00000483923.5(PYROXD2):n.1036C>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000717 in 278,930 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 32)

Exomes 𝑓: 0.0000072 ( 0 hom. )

Consequence

PYROXD2
ENST00000483923.5 non_coding_transcript_exon

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:

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PYROXD2	NM_032709.3 link	c.147+313C>G		intron_variant	Intron 2 of 15	ENST00000370575.5	NP_116098.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PYROXD2	ENST00000483923.5 link	n.1036C>G		non_coding_transcript_exon_variant	Exon 2 of 15	1
PYROXD2	ENST00000370575.5 link	c.147+313C>G		intron_variant	Intron 2 of 15	1	NM_032709.3	ENSP00000359607.4

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

0.00000717

AC:

AN:

278930

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

144356

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

7814

American (AMR)

AF:

0.00

AC:

AN:

9776

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

9522

East Asian (EAS)

AF:

0.00

AC:

AN:

18788

South Asian (SAS)

AF:

0.00

AC:

AN:

21652

European-Finnish (FIN)

AF:

0.00

AC:

AN:

19316

Middle Eastern (MID)

AF:

0.00

AC:

AN:

1398

European-Non Finnish (NFE)

AF:

0.0000115

AC:

AN:

173360

Other (OTH)

AF:

0.00

AC:

AN:

17304

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.475

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

Cov.:

Alfa

AF:

0.00

Hom.:

15769

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

0.025

(source)

DANN

Benign

0.44

PhyloP100

-0.85

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

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over