rs318039

chr5-41475664-C-T

Variant summary

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

The NM_001005473.3(PLCXD3):c.103+34760G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.318 in 534,398 control chromosomes in the GnomAD database, including 30,616 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 0.37 (12554 hom., cov: 32)
  • Exomes 𝑓: 0.30 (18062 hom.)
• Consequence: PLCXD3 NM_001005473.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.937

Genes affected

PLCXD3 (HGNC:31822): (phosphatidylinositol specific phospholipase C X domain containing 3) Predicted to enable phosphoric diester hydrolase activity. Predicted to be involved in lipid catabolic process and signal transduction. Predicted to be located in cytoplasm. Predicted to be active in glutamatergic synapse. [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=-0.77).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.609 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PLCXD3	NM_001005473.3	c.103+34760G>A		intron_variant		ENST00000377801.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PLCXD3	ENST00000377801.8	c.103+34760G>A		intron_variant		1	NM_001005473.3	P1

Frequencies

GnomAD3 genomes AF: 0.374 AC: 56887 AN: 151964 Hom.: 12514 Cov.: 32

Gnomad AFR AF: 0.615

Gnomad AMI AF: 0.404

Gnomad AMR AF: 0.276

Gnomad ASJ AF: 0.362

Gnomad EAS AF: 0.121

Gnomad SAS AF: 0.315

Gnomad FIN AF: 0.232

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.296

Gnomad OTH AF: 0.374

GnomAD3 exomes AF: 0.297 AC: 73137 AN: 246514 Hom.: 12358 AF XY: 0.299 AC XY: 40069 AN XY: 134182

Gnomad AFR exome AF: 0.624

Gnomad AMR exome AF: 0.213

Gnomad ASJ exome AF: 0.375

Gnomad EAS exome AF: 0.119

Gnomad SAS exome AF: 0.340

Gnomad FIN exome AF: 0.248

Gnomad NFE exome AF: 0.295

Gnomad OTH exome AF: 0.311

GnomAD4 exome AF: 0.296 AC: 112977 AN: 382316 Hom.: 18062 Cov.: 0 AF XY: 0.299 AC XY: 65073 AN XY: 217658

Gnomad4 AFR exome AF: 0.613

Gnomad4 AMR exome AF: 0.213

Gnomad4 ASJ exome AF: 0.372

Gnomad4 EAS exome AF: 0.120

Gnomad4 SAS exome AF: 0.337

Gnomad4 FIN exome AF: 0.249

Gnomad4 NFE exome AF: 0.292

Gnomad4 OTH exome AF: 0.315

GnomAD4 genome AF: 0.375 AC: 56975 AN: 152082 Hom.: 12554 Cov.: 32 AF XY: 0.367 AC XY: 27321 AN XY: 74350

Gnomad4 AFR AF: 0.616

Gnomad4 AMR AF: 0.275

Gnomad4 ASJ AF: 0.362

Gnomad4 EAS AF: 0.121

Gnomad4 SAS AF: 0.315

Gnomad4 FIN AF: 0.232

Gnomad4 NFE AF: 0.296

Gnomad4 OTH AF: 0.372

Alfa AF: 0.343 Hom.: 4366

Bravo AF: 0.385

Asia WGS AF: 0.296 AC: 1029 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
Cadd	Benign	4.3
Dann	Benign	0.61

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: rs318039; hg19: chr5-41475766; COSMIC: COSV60605698;