3-141292788-C-T

Position:

• chr3-141292788-C-T

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

The NM_001037172.3(PXYLP1):​c.1026C>T​(p.Phe342=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0901 in 1,613,050 control chromosomes in the GnomAD database, including 6,796 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 0.088 (637 hom., cov: 32)
  • Exomes 𝑓: 0.090 (6159 hom.)
• Consequence: PXYLP1 NM_001037172.3 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.526

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 -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BP7: Synonymous conserved (PhyloP=-0.526 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.105 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PXYLP1	NM_001037172.3	c.1026C>T	p.Phe342=	synonymous_variant	6/6	ENST00000286353.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PXYLP1	ENST00000286353.9	c.1026C>T	p.Phe342=	synonymous_variant	6/6	1	NM_001037172.3	P1
	ENST00000507698.1	n.167-25180G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.0885 AC: 13460 AN: 152100 Hom.: 638 Cov.: 32

Gnomad AFR AF: 0.0887

Gnomad AMI AF: 0.107

Gnomad AMR AF: 0.0954

Gnomad ASJ AF: 0.137

Gnomad EAS AF: 0.113

Gnomad SAS AF: 0.0898

Gnomad FIN AF: 0.0489

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.0881

Gnomad OTH AF: 0.0889

GnomAD3 exomes AF: 0.0843 AC: 21102 AN: 250188 Hom.: 975 AF XY: 0.0866 AC XY: 11709 AN XY: 135180

Gnomad AFR exome AF: 0.0851

Gnomad AMR exome AF: 0.0664

Gnomad ASJ exome AF: 0.130

Gnomad EAS exome AF: 0.101

Gnomad SAS exome AF: 0.0888

Gnomad FIN exome AF: 0.0506

Gnomad NFE exome AF: 0.0880

Gnomad OTH exome AF: 0.0901

GnomAD4 exome AF: 0.0903 AC: 131951 AN: 1460832 Hom.: 6159 Cov.: 31 AF XY: 0.0906 AC XY: 65809 AN XY: 726650

Gnomad4 AFR exome AF: 0.0922

Gnomad4 AMR exome AF: 0.0674

Gnomad4 ASJ exome AF: 0.129

Gnomad4 EAS exome AF: 0.123

Gnomad4 SAS exome AF: 0.0908

Gnomad4 FIN exome AF: 0.0528

Gnomad4 NFE exome AF: 0.0904

Gnomad4 OTH exome AF: 0.0932

GnomAD4 genome AF: 0.0884 AC: 13452 AN: 152218 Hom.: 637 Cov.: 32 AF XY: 0.0865 AC XY: 6439 AN XY: 74424

Gnomad4 AFR AF: 0.0885

Gnomad4 AMR AF: 0.0953

Gnomad4 ASJ AF: 0.137

Gnomad4 EAS AF: 0.113

Gnomad4 SAS AF: 0.0892

Gnomad4 FIN AF: 0.0489

Gnomad4 NFE AF: 0.0881

Gnomad4 OTH AF: 0.0875

Alfa AF: 0.0872 Hom.: 892

Bravo AF: 0.0908

EpiCase AF: 0.0975

EpiControl AF: 0.0945

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	1.5
DANN	Benign	0.86

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: rs3210458; hg19: chr3-141011630; COSMIC: COSV53892670; COSMIC: COSV53892670;