5-41463172-T-C

Variant names:

• chr5-41463172-T-C
• rs318085
• NM_001005473.3:c.103+47252A>G

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+47252A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.86 in 152,000 control chromosomes in the GnomAD database, including 56,634 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 0.86 (56634 hom., cov: 32)
• Consequence: PLCXD3 NM_001005473.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.503
• Publications: 1 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=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.897 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PLCXD3	NM_001005473.3	c.103+47252A>G		intron_variant	Intron 1 of 2	ENST00000377801.8	NP_001005473.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PLCXD3	ENST00000377801.8	c.103+47252A>G		intron_variant	Intron 1 of 2	1	NM_001005473.3	ENSP00000367032.3

Frequencies

GnomAD3 genomes AF: 0.860 AC: 130667 AN: 151882 Hom.: 56586 Cov.: 32

Gnomad AFR AF: 0.772

Gnomad AMI AF: 0.932

Gnomad AMR AF: 0.902

Gnomad ASJ AF: 0.921

Gnomad EAS AF: 0.715

Gnomad SAS AF: 0.799

Gnomad FIN AF: 0.940

Gnomad MID AF: 0.896

Gnomad NFE AF: 0.903

Gnomad OTH AF: 0.874

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

GnomAD4 genome AF: 0.860 AC: 130775 AN: 152000 Hom.: 56634 Cov.: 32 AF XY: 0.860 AC XY: 63924 AN XY: 74298

African (AFR) AF: 0.773 AC: 32024 AN: 41448

American (AMR) AF: 0.902 AC: 13765 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.921 AC: 3195 AN: 3470

East Asian (EAS) AF: 0.715 AC: 3675 AN: 5140

South Asian (SAS) AF: 0.799 AC: 3851 AN: 4818

European-Finnish (FIN) AF: 0.940 AC: 9972 AN: 10614

Middle Eastern (MID) AF: 0.905 AC: 266 AN: 294

European-Non Finnish (NFE) AF: 0.903 AC: 61332 AN: 67930

Other (OTH) AF: 0.874 AC: 1845 AN: 2110

Alfa AF: 0.885 Hom.: 6989

Bravo AF: 0.856

Asia WGS AF: 0.716 AC: 2494 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.2
DANN	Benign	0.53
PhyloP100		-0.50
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: rs318085; hg19: chr5-41463274;