rs9839909

Variant names:

• chr3-171790673-T-C
• rs9839909
• NM_002662.5:c.-32+19726A>G

Variant summary

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

The NM_002662.5(PLD1):​c.-32+19726A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.309 in 152,014 control chromosomes in the GnomAD database, including 7,574 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 0.31 (7574 hom., cov: 32)
• Consequence: PLD1 NM_002662.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.00
• Publications: 3 publications found

Genes affected

PLD1 (HGNC:9067): (phospholipase D1) This gene encodes a phosphatidylcholine-specific phospholipase which catalyzes the hydrolysis of phosphatidylcholine in order to yield phosphatidic acid and choline. The enzyme may play a role in signal transduction and subcellular trafficking. Alternative splicing results in multiple transcript variants with both catalytic and regulatory properties. [provided by RefSeq, Sep 2011]

PLD1 Gene-Disease associations (from GenCC):

• cardiac valvular defect, developmental

  Inheritance: AR Classification: DEFINITIVE, STRONG, MODERATE Submitted by: Ambry Genetics, G2P, Labcorp Genetics (formerly Invitae)
• PLD1-related congenital heart disease

  Inheritance: AR Classification: DEFINITIVE Submitted by: ClinGen

ENSG00000297746 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.35 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002662.5. 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
	PLD1	NM_002662.5	MANE Select	c.-32+19726A>G		intron	N/A	NP_002653.1	Q13393-1
	PLD1	NM_001130081.3		c.-32+19726A>G		intron	N/A	NP_001123553.1	Q13393-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PLD1	ENST00000351298.9	TSL:1 MANE Select	c.-32+19726A>G		intron	N/A	ENSP00000342793.4	Q13393-1
	PLD1	ENST00000356327.9	TSL:1	c.-32+19726A>G		intron	N/A	ENSP00000348681.5	Q13393-2
	PLD1	ENST00000861048.1		c.-32+19726A>G		intron	N/A	ENSP00000531107.1

Frequencies

GnomAD3 genomes AF: 0.309 AC: 46969 AN: 151894 Hom.: 7563 Cov.: 32

Gnomad AFR AF: 0.293

Gnomad AMI AF: 0.341

Gnomad AMR AF: 0.358

Gnomad ASJ AF: 0.234

Gnomad EAS AF: 0.252

Gnomad SAS AF: 0.210

Gnomad FIN AF: 0.413

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.309

Gnomad OTH AF: 0.265

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

GnomAD4 genome AF: 0.309 AC: 47013 AN: 152014 Hom.: 7574 Cov.: 32 AF XY: 0.311 AC XY: 23123 AN XY: 74294

African (AFR) AF: 0.293 AC: 12128 AN: 41446

American (AMR) AF: 0.358 AC: 5474 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.234 AC: 813 AN: 3470

East Asian (EAS) AF: 0.252 AC: 1302 AN: 5160

South Asian (SAS) AF: 0.210 AC: 1013 AN: 4824

European-Finnish (FIN) AF: 0.413 AC: 4364 AN: 10554

Middle Eastern (MID) AF: 0.180 AC: 53 AN: 294

European-Non Finnish (NFE) AF: 0.309 AC: 20990 AN: 67962

Other (OTH) AF: 0.268 AC: 565 AN: 2108

Alfa AF: 0.301 Hom.: 3630

Bravo AF: 0.306

Asia WGS AF: 0.224 AC: 779 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.64
DANN	Benign	0.81
PhyloP100		-1.0
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: rs9839909; hg19: chr3-171508463;