1-242313953-G-A

Variant names:

• chr1-242313953-G-A
• rs3863747
• NM_001372062.1:c.327-25423C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001372062.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PLD5	NM_001372062.1	MANE Select	c.327-25423C>T		intron	N/A	NP_001358991.1
	PLD5	NM_001195811.2		c.141-25423C>T		intron	N/A	NP_001182740.1
	PLD5	NM_001320272.2		c.51-25423C>T		intron	N/A	NP_001307201.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PLD5	ENST00000536534.7	TSL:1 MANE Select	c.327-25423C>T		intron	N/A	ENSP00000440896.1
	PLD5	ENST00000427495.5	TSL:1	c.141-25423C>T		intron	N/A	ENSP00000401285.1
	PLD5	ENST00000442594.6	TSL:5	c.327-25423C>T		intron	N/A	ENSP00000414188.3

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

African (AFR) AF: 0.512 AC: 21168 AN: 41378

American (AMR) AF: 0.231 AC: 3521 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.186 AC: 644 AN: 3468

East Asian (EAS) AF: 0.423 AC: 2177 AN: 5144

South Asian (SAS) AF: 0.293 AC: 1405 AN: 4794

European-Finnish (FIN) AF: 0.238 AC: 2516 AN: 10574

Middle Eastern (MID) AF: 0.259 AC: 76 AN: 294

European-Non Finnish (NFE) AF: 0.224 AC: 15244 AN: 67956

Other (OTH) AF: 0.298 AC: 628 AN: 2110

Alfa AF: 0.253 Hom.: 24445

Bravo AF: 0.324

Asia WGS AF: 0.404 AC: 1405 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.63
DANN	Benign	0.37
PhyloP100		-0.65
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: rs3863747; hg19: chr1-242477255;