10-98406240-C-T

Position:

• chr10-98406240-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.110

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 (HGNC:):

ACMG classification

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
PYROXD2	NM_032709.3	c.315+1342G>A		intron_variant		ENST00000370575.5	NP_116098.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PYROXD2	ENST00000370575.5	c.315+1342G>A		intron_variant		1	NM_032709.3	ENSP00000359607.4
PYROXD2	ENST00000483923.5	n.1217+1342G>A		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.261 AC: 39746 AN: 152014 Hom.: 6437 Cov.: 33

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

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

Other links and lift over

dbSNP: rs17455577; hg19: chr10-100165997;