rs402098

Variant names:

• chr1-242200396-C-G
• rs402098
• NM_001372062.1:c.735+19592G>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 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]

ENSG00000272865 (HGNC:41171):

ACMG classification

Our verdict: Benign. The variant received -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.

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PLD5	NM_001372062.1	MANE Select	c.735+19592G>C		intron	N/A	NP_001358991.1	Q8N7P1-1
	PLD5	NM_001195811.2		c.549+19592G>C		intron	N/A	NP_001182740.1	Q8N7P1-4
	PLD5	NM_001320272.2		c.459+19592G>C		intron	N/A	NP_001307201.1	Q8N7P1-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PLD5	ENST00000536534.7	TSL:1 MANE Select	c.735+19592G>C		intron	N/A	ENSP00000440896.1	Q8N7P1-1
	PLD5	ENST00000427495.5	TSL:1	c.549+19592G>C		intron	N/A	ENSP00000401285.1	Q8N7P1-4
	PLD5	ENST00000442594.6	TSL:5	c.735+19592G>C		intron	N/A	ENSP00000414188.3	Q8N7P1-1

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

African (AFR) AF: 0.951 AC: 39505 AN: 41558

American (AMR) AF: 0.843 AC: 12886 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.830 AC: 2881 AN: 3470

East Asian (EAS) AF: 0.927 AC: 4794 AN: 5174

South Asian (SAS) AF: 0.940 AC: 4536 AN: 4824

European-Finnish (FIN) AF: 0.824 AC: 8730 AN: 10598

Middle Eastern (MID) AF: 0.823 AC: 242 AN: 294

European-Non Finnish (NFE) AF: 0.773 AC: 52558 AN: 67994

Other (OTH) AF: 0.841 AC: 1776 AN: 2112

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.92
DANN	Benign	0.75
PhyloP100		-0.037
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: rs402098; hg19: chr1-242363698;