ENST00000483923.5:n.1036C>T

Variant names:

• chr10-98410626-G-A
• rs6584202
• ENST00000483923.5:n.1036C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000483923.5(PYROXD2):​n.1036C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.323 in 430,030 control chromosomes in the GnomAD database, including 26,272 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 0.38 (12669 hom., cov: 32)
  • Exomes 𝑓: 0.29 (13603 hom.)
• Consequence: PYROXD2 ENST00000483923.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.855
• Publications: 20 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.589 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000483923.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PYROXD2	NM_032709.3	MANE Select	c.147+313C>T		intron	N/A	NP_116098.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PYROXD2	ENST00000483923.5	TSL:1	n.1036C>T		non_coding_transcript_exon	Exon 2 of 15
	PYROXD2	ENST00000370575.5	TSL:1 MANE Select	c.147+313C>T		intron	N/A	ENSP00000359607.4

Frequencies

GnomAD3 genomes AF: 0.381 AC: 57821 AN: 151888 Hom.: 12644 Cov.: 32

Gnomad AFR AF: 0.595

Gnomad AMI AF: 0.272

Gnomad AMR AF: 0.391

Gnomad ASJ AF: 0.354

Gnomad EAS AF: 0.440

Gnomad SAS AF: 0.487

Gnomad FIN AF: 0.236

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.262

Gnomad OTH AF: 0.353

GnomAD4 exome AF: 0.292 AC: 81204 AN: 278024 Hom.: 13603 Cov.: 3 AF XY: 0.298 AC XY: 42815 AN XY: 143856

African (AFR) AF: 0.585 AC: 4551 AN: 7778

American (AMR) AF: 0.376 AC: 3659 AN: 9732

Ashkenazi Jewish (ASJ) AF: 0.326 AC: 3096 AN: 9484

East Asian (EAS) AF: 0.386 AC: 7208 AN: 18696

South Asian (SAS) AF: 0.470 AC: 10133 AN: 21540

European-Finnish (FIN) AF: 0.212 AC: 4082 AN: 19276

Middle Eastern (MID) AF: 0.360 AC: 502 AN: 1394

European-Non Finnish (NFE) AF: 0.246 AC: 42520 AN: 172866

Other (OTH) AF: 0.316 AC: 5453 AN: 17258

GnomAD4 genome AF: 0.381 AC: 57895 AN: 152006 Hom.: 12669 Cov.: 32 AF XY: 0.382 AC XY: 28401 AN XY: 74298

African (AFR) AF: 0.595 AC: 24681 AN: 41450

American (AMR) AF: 0.391 AC: 5981 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.354 AC: 1229 AN: 3470

East Asian (EAS) AF: 0.439 AC: 2263 AN: 5150

South Asian (SAS) AF: 0.486 AC: 2340 AN: 4816

European-Finnish (FIN) AF: 0.236 AC: 2491 AN: 10568

Middle Eastern (MID) AF: 0.354 AC: 104 AN: 294

European-Non Finnish (NFE) AF: 0.262 AC: 17816 AN: 67944

Other (OTH) AF: 0.352 AC: 742 AN: 2106

Alfa AF: 0.329 Hom.: 15769

Bravo AF: 0.396

Asia WGS AF: 0.466 AC: 1618 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.051
DANN	Benign	0.33
PhyloP100		-0.85
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs6584202; hg19: chr10-100170383;