rs11708205

Variant names:

• chr3-171753574-T-C
• rs11708205
• NM_002662.5:c.-31-15492A>G

Variant summary

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

The NM_002662.5(PLD1):​c.-31-15492A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.138 in 152,144 control chromosomes in the GnomAD database, including 1,521 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 0.14 (1521 hom., cov: 32)
• Consequence: PLD1 NM_002662.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11

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 (SAS) allele frequency at 95% confidence interval = 0.208 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PLD1	NM_002662.5	c.-31-15492A>G		intron_variant	Intron 1 of 26	ENST00000351298.9	NP_002653.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PLD1	ENST00000351298.9	c.-31-15492A>G		intron_variant	Intron 1 of 26	1	NM_002662.5	ENSP00000342793.4

Frequencies

GnomAD3 genomes AF: 0.138 AC: 21001 AN: 152026 Hom.: 1516 Cov.: 32

Gnomad AFR AF: 0.123

Gnomad AMI AF: 0.237

Gnomad AMR AF: 0.105

Gnomad ASJ AF: 0.130

Gnomad EAS AF: 0.125

Gnomad SAS AF: 0.219

Gnomad FIN AF: 0.140

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.148

Gnomad OTH AF: 0.152

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

GnomAD4 genome AF: 0.138 AC: 21016 AN: 152144 Hom.: 1521 Cov.: 32 AF XY: 0.140 AC XY: 10400 AN XY: 74390

Gnomad4 AFR AF: 0.124

Gnomad4 AMR AF: 0.105

Gnomad4 ASJ AF: 0.130

Gnomad4 EAS AF: 0.125

Gnomad4 SAS AF: 0.219

Gnomad4 FIN AF: 0.140

Gnomad4 NFE AF: 0.148

Gnomad4 OTH AF: 0.150

Alfa AF: 0.148 Hom.: 890

Bravo AF: 0.133

Asia WGS AF: 0.158 AC: 547 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.8
DANN	Benign	0.47

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: rs11708205; hg19: chr3-171471364;