3-111702663-T-C

Variant summary

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

The ENST00000477665.2(PLCXD2):c.164-5263T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.968 in 152,240 control chromosomes in the GnomAD database, including 71,404 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 0.97 (71404 hom., cov: 31)
• Consequence: PLCXD2 ENST00000477665.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.151

Genes affected

PLCXD2 (HGNC:26462): (phosphatidylinositol specific phospholipase C X domain containing 2) Predicted to enable phosphoric diester hydrolase activity. Predicted to be involved in lipid catabolic process and signal transduction. Predicted to be located in nucleus. [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=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PLCXD2	NM_001413064.1	c.164-5263T>C		intron_variant		ENST00000636933.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PLCXD2	ENST00000636933.2	c.164-5263T>C		intron_variant		5	NM_001413064.1	P1
PLCXD2	ENST00000393934.7	c.164-5263T>C		intron_variant		1
PLCXD2	ENST00000477665.2	c.164-5263T>C		intron_variant		1
PLCXD2	ENST00000468174.1	n.204-5263T>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.968 AC: 147329 AN: 152126 Hom.: 71356 Cov.: 31

Gnomad AFR AF: 0.941

Gnomad AMI AF: 0.997

Gnomad AMR AF: 0.980

Gnomad ASJ AF: 0.987

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.973

Gnomad FIN AF: 0.995

Gnomad MID AF: 0.984

Gnomad NFE AF: 0.974

Gnomad OTH AF: 0.982

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

GnomAD4 genome AF: 0.968 AC: 147433 AN: 152240 Hom.: 71404 Cov.: 31 AF XY: 0.970 AC XY: 72178 AN XY: 74428

Gnomad4 AFR AF: 0.941

Gnomad4 AMR AF: 0.980

Gnomad4 ASJ AF: 0.987

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.973

Gnomad4 FIN AF: 0.995

Gnomad4 NFE AF: 0.974

Gnomad4 OTH AF: 0.982

Alfa AF: 0.972 Hom.: 32465

Bravo AF: 0.969

Asia WGS AF: 0.985 AC: 3425 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	4.3
Dann	Benign	0.35

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: rs1513334; hg19: chr3-111421510;