rs3863747

chr1-242313953-G-Achr1-242313953-G-C

Variant summary

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

The NM_001372062.1(PLD5):c.327-25423C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.313 in 151,894 control chromosomes in the GnomAD database, including 8,799 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 (8799 hom., cov: 31)
• Consequence: PLD5 NM_001372062.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.648

Genes affected

PLD5 (HGNC:26879): (phospholipase D family member 5) Predicted to enable catalytic activity. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.506 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PLD5	NM_001372062.1	c.327-25423C>T		intron_variant		ENST00000536534.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PLD5	ENST00000536534.7	c.327-25423C>T		intron_variant		1	NM_001372062.1	P1

Frequencies

GnomAD3 genomes AF: 0.313 AC: 47476 AN: 151776 Hom.: 8773 Cov.: 31

Gnomad AFR AF: 0.511

Gnomad AMI AF: 0.187

Gnomad AMR AF: 0.231

Gnomad ASJ AF: 0.186

Gnomad EAS AF: 0.425

Gnomad SAS AF: 0.291

Gnomad FIN AF: 0.238

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.224

Gnomad OTH AF: 0.292

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

GnomAD4 genome AF: 0.313 AC: 47549 AN: 151894 Hom.: 8799 Cov.: 31 AF XY: 0.313 AC XY: 23214 AN XY: 74240

Gnomad4 AFR AF: 0.512

Gnomad4 AMR AF: 0.231

Gnomad4 ASJ AF: 0.186

Gnomad4 EAS AF: 0.423

Gnomad4 SAS AF: 0.293

Gnomad4 FIN AF: 0.238

Gnomad4 NFE AF: 0.224

Gnomad4 OTH AF: 0.298

Alfa AF: 0.241 Hom.: 10072

Bravo AF: 0.324

Asia WGS AF: 0.404 AC: 1405 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	0.63
Dann	Benign	0.37

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: rs3863747; hg19: chr1-242477255;