rs9839909

Positions:

• chr3-171790673-T-C

Variant summary

Our verdict is Benign. Variant got -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

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]

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PLD1	NM_002662.5	c.-32+19726A>G		intron_variant		ENST00000351298.9	NP_002653.1
PLD1	NM_001130081.3	c.-32+19726A>G		intron_variant			NP_001123553.1
PLD1	XM_047448316.1	c.-32+6515A>G		intron_variant			XP_047304272.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PLD1	ENST00000351298.9	c.-32+19726A>G		intron_variant		1	NM_002662.5	ENSP00000342793	A1

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

Gnomad4 AFR AF: 0.293

Gnomad4 AMR AF: 0.358

Gnomad4 ASJ AF: 0.234

Gnomad4 EAS AF: 0.252

Gnomad4 SAS AF: 0.210

Gnomad4 FIN AF: 0.413

Gnomad4 NFE AF: 0.309

Gnomad4 OTH AF: 0.268

Alfa AF: 0.301 Hom.: 3286

Bravo AF: 0.306

Asia WGS AF: 0.224 AC: 779 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.64
DANN	Benign	0.81

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: rs9839909; hg19: chr3-171508463;