rs2147901

Positions:

• chr10-98405739-C-A
• chr10-98405739-C-G

Variant summary

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

The NM_032709.3(PYROXD2):​c.315+1843G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.371 in 152,038 control chromosomes in the GnomAD database, including 11,808 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 0.37 (11808 hom., cov: 33)
• Consequence: PYROXD2 NM_032709.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.555 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PYROXD2	NM_032709.3	c.315+1843G>T		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+1843G>T		intron_variant		1	NM_032709.3	ENSP00000359607	P1
PYROXD2	ENST00000483923.5	n.1217+1843G>T		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.371 AC: 56314 AN: 151920 Hom.: 11782 Cov.: 33

Gnomad AFR AF: 0.560

Gnomad AMI AF: 0.274

Gnomad AMR AF: 0.387

Gnomad ASJ AF: 0.354

Gnomad EAS AF: 0.438

Gnomad SAS AF: 0.487

Gnomad FIN AF: 0.237

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.262

Gnomad OTH AF: 0.346

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.371 AC: 56389 AN: 152038 Hom.: 11808 Cov.: 33 AF XY: 0.372 AC XY: 27672 AN XY: 74320

Gnomad4 AFR AF: 0.561

Gnomad4 AMR AF: 0.387

Gnomad4 ASJ AF: 0.354

Gnomad4 EAS AF: 0.438

Gnomad4 SAS AF: 0.486

Gnomad4 FIN AF: 0.237

Gnomad4 NFE AF: 0.262

Gnomad4 OTH AF: 0.345

Alfa AF: 0.299 Hom.: 2999

Bravo AF: 0.385

Asia WGS AF: 0.466 AC: 1616 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.44
DANN	Benign	0.42

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		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: rs2147901; hg19: chr10-100165496;