rs2147897

Variant names:

• chr10-98388056-G-C
• rs2147897
• NM_032709.3:c.1447+298C>G

Your query was ambiguous. Multiple possible variants found:

• chr10-98388056-G-C
• chr10-98388056-G-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_032709.3(PYROXD2):​c.1447+298C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000017 in 176,724 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 32)
  • Exomes 𝑓: 0.000017 (0 hom.)
• Consequence: PYROXD2 NM_032709.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.297
• 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PYROXD2	NM_032709.3	c.1447+298C>G		intron_variant	Intron 13 of 15	ENST00000370575.5	NP_116098.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PYROXD2	ENST00000370575.5	c.1447+298C>G		intron_variant	Intron 13 of 15	1	NM_032709.3	ENSP00000359607.4
PYROXD2	ENST00000483923.5	n.2334-749C>G		intron_variant	Intron 12 of 14	1
PYROXD2	ENST00000464808.1	n.112C>G		non_coding_transcript_exon_variant	Exon 2 of 3	3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.0000170 AC: 3 AN: 176724 Hom.: 0 Cov.: 0 AF XY: 0.0000106 AC XY: 1 AN XY: 94672

African (AFR) AF: 0.00 AC: 0 AN: 3500

American (AMR) AF: 0.00 AC: 0 AN: 6334

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 4898

East Asian (EAS) AF: 0.00 AC: 0 AN: 6028

South Asian (SAS) AF: 0.00 AC: 0 AN: 28240

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 9656

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 726

European-Non Finnish (NFE) AF: 0.0000279 AC: 3 AN: 107544

Other (OTH) AF: 0.00 AC: 0 AN: 9798

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 5258

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.1
DANN	Benign	0.32
PhyloP100		0.30

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: rs2147897; hg19: chr10-100147813;