3-141260569-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001037172.3(PXYLP1):c.79+315A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0417 in 152,176 control chromosomes in the GnomAD database, including 298 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 0.042 (298 hom., cov: 33)
• Consequence: PXYLP1 NM_001037172.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0760

Genes affected

PXYLP1 (HGNC:26303): (2-phosphoxylose phosphatase 1) Enables phosphatase activity. Involved in chondroitin sulfate proteoglycan biosynthetic process; glycosaminoglycan biosynthetic process; and positive regulation of heparan sulfate proteoglycan biosynthetic process. Located in Golgi apparatus. [provided by Alliance of Genome Resources, Apr 2022]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.191 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PXYLP1	NM_001037172.3	c.79+315A>G		intron_variant		ENST00000286353.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PXYLP1	ENST00000286353.9	c.79+315A>G		intron_variant		1	NM_001037172.3	P1
	ENST00000663611.1	n.173-9226T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0417 AC: 6339 AN: 152060 Hom.: 297 Cov.: 33

Gnomad AFR AF: 0.0821

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0676

Gnomad ASJ AF: 0.0121

Gnomad EAS AF: 0.201

Gnomad SAS AF: 0.0325

Gnomad FIN AF: 0.0122

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.00650

Gnomad OTH AF: 0.0441

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

GnomAD4 genome AF: 0.0417 AC: 6348 AN: 152176 Hom.: 298 Cov.: 33 AF XY: 0.0430 AC XY: 3199 AN XY: 74422

Gnomad4 AFR AF: 0.0818

Gnomad4 AMR AF: 0.0684

Gnomad4 ASJ AF: 0.0121

Gnomad4 EAS AF: 0.201

Gnomad4 SAS AF: 0.0323

Gnomad4 FIN AF: 0.0122

Gnomad4 NFE AF: 0.00650

Gnomad4 OTH AF: 0.0441

Alfa AF: 0.0133 Hom.: 111

Bravo AF: 0.0485

Asia WGS AF: 0.115 AC: 399 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	5.6
Dann	Benign	0.63

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: rs16851254; hg19: chr3-140979411;