rs942812

chr10-98393907-C-Achr10-98393907-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.786-824G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.153 in 152,084 control chromosomes in the GnomAD database, including 3,504 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 0.15 (3504 hom., cov: 32)
• Consequence: PYROXD2 NM_032709.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.56

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 = 0.376 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PYROXD2	NM_032709.3	c.786-824G>T		intron_variant		ENST00000370575.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PYROXD2	ENST00000370575.5	c.786-824G>T		intron_variant		1	NM_032709.3	P1
PYROXD2	ENST00000483923.5	n.1688-824G>T		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.153 AC: 23230 AN: 151966 Hom.: 3500 Cov.: 32

Gnomad AFR AF: 0.381

Gnomad AMI AF: 0.00440

Gnomad AMR AF: 0.171

Gnomad ASJ AF: 0.0565

Gnomad EAS AF: 0.127

Gnomad SAS AF: 0.0952

Gnomad FIN AF: 0.0739

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0365

Gnomad OTH AF: 0.130

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

GnomAD4 genome AF: 0.153 AC: 23275 AN: 152084 Hom.: 3504 Cov.: 32 AF XY: 0.153 AC XY: 11400 AN XY: 74352

Gnomad4 AFR AF: 0.381

Gnomad4 AMR AF: 0.171

Gnomad4 ASJ AF: 0.0565

Gnomad4 EAS AF: 0.127

Gnomad4 SAS AF: 0.0945

Gnomad4 FIN AF: 0.0739

Gnomad4 NFE AF: 0.0365

Gnomad4 OTH AF: 0.130

Alfa AF: 0.0447 Hom.: 94

Bravo AF: 0.173

Asia WGS AF: 0.149 AC: 516 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	0.0080
Dann	Benign	0.50

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: rs942812; hg19: chr10-100153664; COSMIC: COSV65330738; COSMIC: COSV65330738;