rs17455577

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_032709.3(PYROXD2):​c.315+1342G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.261 in 152,132 control chromosomes in the GnomAD database, including 6,442 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 0.26 ( 6442 hom., cov: 33)

Consequence

PYROXD2
NM_032709.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.110
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.334 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
PYROXD2NM_032709.3 linkuse as main transcriptc.315+1342G>A intron_variant ENST00000370575.5 NP_116098.2 Q8N2H3

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
PYROXD2ENST00000370575.5 linkuse as main transcriptc.315+1342G>A intron_variant 1 NM_032709.3 ENSP00000359607.4 Q8N2H3
PYROXD2ENST00000483923.5 linkuse as main transcriptn.1217+1342G>A intron_variant 1

Frequencies

GnomAD3 genomes
AF:
0.261
AC:
39746
AN:
152014
Hom.:
6437
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0873
Gnomad AMI
AF:
0.290
Gnomad AMR
AF:
0.225
Gnomad ASJ
AF:
0.242
Gnomad EAS
AF:
0.280
Gnomad SAS
AF:
0.289
Gnomad FIN
AF:
0.490
Gnomad MID
AF:
0.234
Gnomad NFE
AF:
0.338
Gnomad OTH
AF:
0.254
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.261
AC:
39758
AN:
152132
Hom.:
6442
Cov.:
33
AF XY:
0.268
AC XY:
19950
AN XY:
74366
show subpopulations
Gnomad4 AFR
AF:
0.0871
Gnomad4 AMR
AF:
0.225
Gnomad4 ASJ
AF:
0.242
Gnomad4 EAS
AF:
0.281
Gnomad4 SAS
AF:
0.289
Gnomad4 FIN
AF:
0.490
Gnomad4 NFE
AF:
0.338
Gnomad4 OTH
AF:
0.257
Alfa
AF:
0.311
Hom.:
7007
Bravo
AF:
0.235
Asia WGS
AF:
0.268
AC:
932
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
1.6
DANN
Benign
0.83

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs17455577; hg19: chr10-100165997; API