3-111702663-T-C

Variant names:

• chr3-111702663-T-C
• rs1513334
• NM_001413064.1:c.164-5263T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001413064.1(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 NM_001413064.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.151
• Publications: 2 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001413064.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PLCXD2	NM_001413064.1	MANE Select	c.164-5263T>C		intron	N/A	NP_001399993.1	A0A1B0GW80

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PLCXD2	ENST00000636933.2	TSL:5 MANE Select	c.164-5263T>C		intron	N/A	ENSP00000490816.1	A0A1B0GW80
	PLCXD2	ENST00000477665.2	TSL:1	c.164-5263T>C		intron	N/A	ENSP00000420686.1	Q0VAA5-1
	PLCXD2	ENST00000393934.7	TSL:1	c.164-5263T>C		intron	N/A	ENSP00000377511.3	Q0VAA5-2

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

African (AFR) AF: 0.941 AC: 39034 AN: 41500

American (AMR) AF: 0.980 AC: 14981 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.987 AC: 3427 AN: 3472

East Asian (EAS) AF: 0.999 AC: 5178 AN: 5182

South Asian (SAS) AF: 0.973 AC: 4694 AN: 4826

European-Finnish (FIN) AF: 0.995 AC: 10565 AN: 10620

Middle Eastern (MID) AF: 0.983 AC: 289 AN: 294

European-Non Finnish (NFE) AF: 0.974 AC: 66281 AN: 68034

Other (OTH) AF: 0.982 AC: 2075 AN: 2112

Alfa AF: 0.972 Hom.: 36496

Bravo AF: 0.969

Asia WGS AF: 0.985 AC: 3425 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	4.3
DANN	Benign	0.35
PhyloP100		-0.15
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: rs1513334; hg19: chr3-111421510;