rs402098

Positions:

• chr1-242200396-C-G

Variant summary

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

The NM_001372062.1(PLD5):​c.735+19592G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.845 in 152,224 control chromosomes in the GnomAD database, including 54,798 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 0.84 (54798 hom., cov: 32)
• Consequence: PLD5 NM_001372062.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0370

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.943 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PLD5	NM_001372062.1	c.735+19592G>C		intron_variant		ENST00000536534.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PLD5	ENST00000536534.7	c.735+19592G>C		intron_variant		1	NM_001372062.1	P1
	ENST00000608241.1	n.437+8092C>G		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.845 AC: 128511 AN: 152106 Hom.: 54744 Cov.: 32

Gnomad AFR AF: 0.951

Gnomad AMI AF: 0.783

Gnomad AMR AF: 0.843

Gnomad ASJ AF: 0.830

Gnomad EAS AF: 0.927

Gnomad SAS AF: 0.941

Gnomad FIN AF: 0.824

Gnomad MID AF: 0.826

Gnomad NFE AF: 0.773

Gnomad OTH AF: 0.842

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

GnomAD4 genome AF: 0.845 AC: 128622 AN: 152224 Hom.: 54798 Cov.: 32 AF XY: 0.850 AC XY: 63256 AN XY: 74422

Gnomad4 AFR AF: 0.951

Gnomad4 AMR AF: 0.843

Gnomad4 ASJ AF: 0.830

Gnomad4 EAS AF: 0.927

Gnomad4 SAS AF: 0.940

Gnomad4 FIN AF: 0.824

Gnomad4 NFE AF: 0.773

Gnomad4 OTH AF: 0.841

Alfa AF: 0.817 Hom.: 6329

Bravo AF: 0.850

Asia WGS AF: 0.915 AC: 3183 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.92
DANN	Benign	0.75

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: rs402098; hg19: chr1-242363698;