rs318039

Variant names:

• chr5-41475664-C-T
• rs318039
• NM_001005473.3:c.103+34760G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 10 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001005473.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PLCXD3	NM_001005473.3	MANE Select	c.103+34760G>A		intron	N/A	NP_001005473.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PLCXD3	ENST00000377801.8	TSL:1 MANE Select	c.103+34760G>A		intron	N/A	ENSP00000367032.3

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

GnomAD2 exomes AF: 0.297 AC: 73137 AN: 246514 AF XY: 0.299

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 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

African (AFR) AF: 0.613 AC: 6439 AN: 10506

American (AMR) AF: 0.213 AC: 7722 AN: 36288

Ashkenazi Jewish (ASJ) AF: 0.372 AC: 4372 AN: 11738

East Asian (EAS) AF: 0.120 AC: 1584 AN: 13176

South Asian (SAS) AF: 0.337 AC: 22493 AN: 66738

European-Finnish (FIN) AF: 0.249 AC: 8045 AN: 32308

Middle Eastern (MID) AF: 0.346 AC: 986 AN: 2852

European-Non Finnish (NFE) AF: 0.292 AC: 56072 AN: 191996

Other (OTH) AF: 0.315 AC: 5264 AN: 16714

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

African (AFR) AF: 0.616 AC: 25529 AN: 41460

American (AMR) AF: 0.275 AC: 4203 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.362 AC: 1257 AN: 3470

East Asian (EAS) AF: 0.121 AC: 623 AN: 5168

South Asian (SAS) AF: 0.315 AC: 1517 AN: 4818

European-Finnish (FIN) AF: 0.232 AC: 2454 AN: 10580

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.296 AC: 20136 AN: 67992

Other (OTH) AF: 0.372 AC: 783 AN: 2106

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	4.3
DANN	Benign	0.61
PhyloP100		-0.94
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: rs318039; hg19: chr5-41475766; COSMIC: COSV60605698;