3-141260569-A-G

Variant names:

• chr3-141260569-A-G
• rs16851254
• NM_001037172.3:c.79+315A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

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]

ENSG00000287155 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
PXYLP1	NM_001037172.3	c.79+315A>G		intron_variant	Intron 2 of 5	ENST00000286353.9	NP_001032249.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PXYLP1	ENST00000286353.9	c.79+315A>G		intron_variant	Intron 2 of 5	1	NM_001037172.3	ENSP00000286353.4

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

African (AFR) AF: 0.0818 AC: 3388 AN: 41436

American (AMR) AF: 0.0684 AC: 1047 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0121 AC: 42 AN: 3468

East Asian (EAS) AF: 0.201 AC: 1040 AN: 5178

South Asian (SAS) AF: 0.0323 AC: 156 AN: 4830

European-Finnish (FIN) AF: 0.0122 AC: 130 AN: 10620

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.00650 AC: 442 AN: 68030

Other (OTH) AF: 0.0441 AC: 93 AN: 2110

Alfa AF: 0.0186 Hom.: 423

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
PhyloP100		0.076
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: rs16851254; hg19: chr3-140979411;