rs8066520

Variant names:

• chr17-29049573-G-A
• rs8066520
• NM_016518.3:c.264-3347G>A

Your query was ambiguous. Multiple possible variants found:

• chr17-29049573-G-A
• chr17-29049573-G-C

Variant summary

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

The NM_016518.3(PIPOX):​c.264-3347G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.223 in 152,116 control chromosomes in the GnomAD database, including 4,502 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 0.22 (4502 hom., cov: 32)
• Consequence: PIPOX NM_016518.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.13
• Publications: 5 publications found

Genes affected

PIPOX (HGNC:17804): (pipecolic acid and sarcosine oxidase) Enables L-pipecolate oxidase activity and sarcosine oxidase activity. Involved in L-lysine catabolic process to acetyl-CoA via L-pipecolate. Located in peroxisome. [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=-0.67).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.37 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_016518.3. 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
	PIPOX	NM_016518.3	MANE Select	c.264-3347G>A		intron	N/A	NP_057602.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PIPOX	ENST00000323372.9	TSL:1 MANE Select	c.264-3347G>A		intron	N/A	ENSP00000317721.4
	PIPOX	ENST00000469082.1	TSL:5	c.66-3347G>A		intron	N/A	ENSP00000465329.1
	PIPOX	ENST00000466889.5	TSL:2	c.66-3347G>A		intron	N/A	ENSP00000465428.1

Frequencies

GnomAD3 genomes AF: 0.222 AC: 33798 AN: 151998 Hom.: 4493 Cov.: 32

Gnomad AFR AF: 0.376

Gnomad AMI AF: 0.205

Gnomad AMR AF: 0.179

Gnomad ASJ AF: 0.202

Gnomad EAS AF: 0.263

Gnomad SAS AF: 0.146

Gnomad FIN AF: 0.187

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.149

Gnomad OTH AF: 0.204

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

GnomAD4 genome AF: 0.223 AC: 33846 AN: 152116 Hom.: 4502 Cov.: 32 AF XY: 0.222 AC XY: 16545 AN XY: 74388

African (AFR) AF: 0.375 AC: 15563 AN: 41454

American (AMR) AF: 0.179 AC: 2727 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.202 AC: 700 AN: 3470

East Asian (EAS) AF: 0.263 AC: 1360 AN: 5180

South Asian (SAS) AF: 0.146 AC: 705 AN: 4822

European-Finnish (FIN) AF: 0.187 AC: 1981 AN: 10592

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.149 AC: 10139 AN: 68004

Other (OTH) AF: 0.208 AC: 439 AN: 2112

Alfa AF: 0.149 Hom.: 1041

Bravo AF: 0.229

Asia WGS AF: 0.233 AC: 808 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	13
DANN	Benign	0.57
PhyloP100		1.1
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: rs8066520; hg19: chr17-27376591;