chr17-29049573-G-A

Position:

• chr17-29049573-G-A

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PIPOX	NM_016518.3	c.264-3347G>A		intron_variant		ENST00000323372.9	NP_057602.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PIPOX	ENST00000323372.9	c.264-3347G>A		intron_variant		1	NM_016518.3	ENSP00000317721	P1

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

Gnomad4 AFR AF: 0.375

Gnomad4 AMR AF: 0.179

Gnomad4 ASJ AF: 0.202

Gnomad4 EAS AF: 0.263

Gnomad4 SAS AF: 0.146

Gnomad4 FIN AF: 0.187

Gnomad4 NFE AF: 0.149

Gnomad4 OTH AF: 0.208

Alfa AF: 0.147 Hom.: 929

Bravo AF: 0.229

Asia WGS AF: 0.233 AC: 808 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	13
DANN	Benign	0.57

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: rs8066520; hg19: chr17-27376591;