rs12151243

chr19-40356965-G-T

Variant summary

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

The NM_012268.4(PLD3):c.-279+8197G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.158 in 152,050 control chromosomes in the GnomAD database, including 2,023 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 0.16 (2023 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: PLD3 NM_012268.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.571

Genes affected

PLD3 (HGNC:17158): (phospholipase D family member 3) This gene encodes a member of the phospholipase D (PLD) family of enzymes that catalyze the hydrolysis of membrane phospholipids. The encoded protein is a single-pass type II membrane protein and contains two PLD phosphodiesterase domains. This protein influences processing of amyloid-beta precursor protein. Mutations in this gene are associated with Alzheimer disease risk. Alternatively spliced transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Apr 2014]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.175 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PLD3	NM_012268.4	c.-279+8197G>T		intron_variant		ENST00000409735.9
PLD3	NM_001031696.4	c.-99+8241G>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PLD3	ENST00000409735.9	c.-279+8197G>T		intron_variant		1	NM_012268.4	P1
	ENST00000622968.1	n.1124G>T		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.158 AC: 23933 AN: 151932 Hom.: 2017 Cov.: 32

Gnomad AFR AF: 0.178

Gnomad AMI AF: 0.192

Gnomad AMR AF: 0.130

Gnomad ASJ AF: 0.158

Gnomad EAS AF: 0.136

Gnomad SAS AF: 0.106

Gnomad FIN AF: 0.196

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.150

Gnomad OTH AF: 0.155

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 4 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 4

Gnomad4 FIN exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.158 AC: 23962 AN: 152050 Hom.: 2023 Cov.: 32 AF XY: 0.157 AC XY: 11689 AN XY: 74316

Gnomad4 AFR AF: 0.178

Gnomad4 AMR AF: 0.130

Gnomad4 ASJ AF: 0.158

Gnomad4 EAS AF: 0.137

Gnomad4 SAS AF: 0.106

Gnomad4 FIN AF: 0.196

Gnomad4 NFE AF: 0.150

Gnomad4 OTH AF: 0.155

Alfa AF: 0.147 Hom.: 1715

Bravo AF: 0.152

Asia WGS AF: 0.124 AC: 430 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.65
Dann	Benign	0.62

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: rs12151243; hg19: chr19-40862872;