rs17455577

Variant names:

• chr10-98406240-C-T
• rs17455577
• NM_032709.3:c.315+1342G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 11 publications found

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

Our verdict: Benign. The variant received -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.

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.315+1342G>A		intron	N/A	NP_116098.2	Q8N2H3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PYROXD2	ENST00000370575.5	TSL:1 MANE Select	c.315+1342G>A		intron	N/A	ENSP00000359607.4	Q8N2H3
	PYROXD2	ENST00000483923.5	TSL:1	n.1217+1342G>A		intron	N/A
	PYROXD2	ENST00000906254.1		c.315+1342G>A		intron	N/A	ENSP00000576313.1

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

African (AFR) AF: 0.0871 AC: 3613 AN: 41502

American (AMR) AF: 0.225 AC: 3440 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.242 AC: 841 AN: 3470

East Asian (EAS) AF: 0.281 AC: 1452 AN: 5174

South Asian (SAS) AF: 0.289 AC: 1394 AN: 4824

European-Finnish (FIN) AF: 0.490 AC: 5181 AN: 10564

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.338 AC: 22962 AN: 67984

Other (OTH) AF: 0.257 AC: 544 AN: 2116

Alfa AF: 0.298 Hom.: 18736

Bravo AF: 0.235

Asia WGS AF: 0.268 AC: 932 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.6
DANN	Benign	0.83
PhyloP100		-0.11
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs17455577; hg19: chr10-100165997;