chr3-111704282-G-C

Variant names:

• chr3-111704282-G-C
• rs4450776
• NM_001413064.1:c.164-3644G>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.164-3644G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.952 in 152,328 control chromosomes in the GnomAD database, including 69,141 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 0.95 (69141 hom., cov: 32)
• Consequence: PLCXD2 NM_001413064.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.62
• Publications: 10 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=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.956 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PLCXD2	NM_001413064.1	MANE Select	c.164-3644G>C		intron	N/A	NP_001399993.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PLCXD2	ENST00000636933.2	TSL:5 MANE Select	c.164-3644G>C		intron	N/A	ENSP00000490816.1
	PLCXD2	ENST00000477665.2	TSL:1	c.164-3644G>C		intron	N/A	ENSP00000420686.1
	PLCXD2	ENST00000393934.7	TSL:1	c.164-3644G>C		intron	N/A	ENSP00000377511.3

Frequencies

GnomAD3 genomes AF: 0.953 AC: 144985 AN: 152210 Hom.: 69098 Cov.: 32

Gnomad AFR AF: 0.944

Gnomad AMI AF: 0.988

Gnomad AMR AF: 0.943

Gnomad ASJ AF: 0.963

Gnomad EAS AF: 0.880

Gnomad SAS AF: 0.902

Gnomad FIN AF: 0.989

Gnomad MID AF: 0.978

Gnomad NFE AF: 0.962

Gnomad OTH AF: 0.971

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

GnomAD4 genome AF: 0.952 AC: 145084 AN: 152328 Hom.: 69141 Cov.: 32 AF XY: 0.953 AC XY: 70946 AN XY: 74478

African (AFR) AF: 0.944 AC: 39218 AN: 41566

American (AMR) AF: 0.942 AC: 14422 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.963 AC: 3342 AN: 3472

East Asian (EAS) AF: 0.880 AC: 4557 AN: 5180

South Asian (SAS) AF: 0.901 AC: 4347 AN: 4826

European-Finnish (FIN) AF: 0.989 AC: 10504 AN: 10624

Middle Eastern (MID) AF: 0.973 AC: 286 AN: 294

European-Non Finnish (NFE) AF: 0.962 AC: 65458 AN: 68040

Other (OTH) AF: 0.970 AC: 2049 AN: 2112

Alfa AF: 0.957 Hom.: 33239

Bravo AF: 0.948

Asia WGS AF: 0.870 AC: 3026 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.43
DANN	Benign	0.56
PhyloP100		-1.6
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: rs4450776; hg19: chr3-111423129;