chr1-242437304-A-G

Variant names:

• chr1-242437304-A-G
• rs2654879
• NM_001372062.1:c.189+86784T>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.189+86784T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.561 in 151,976 control chromosomes in the GnomAD database, including 24,683 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 0.56 (24683 hom., cov: 32)
• Consequence: PLD5 NM_001372062.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.809
• Publications: 3 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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.693 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.189+86784T>C		intron	N/A	NP_001358991.1
	PLD5	NM_001195811.2		c.3+12050T>C		intron	N/A	NP_001182740.1
	PLD5	NM_001320272.2		c.-95+86784T>C		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.189+86784T>C		intron	N/A	ENSP00000440896.1
	PLD5	ENST00000427495.5	TSL:1	c.3+12050T>C		intron	N/A	ENSP00000401285.1
	PLD5	ENST00000442594.6	TSL:5	c.189+86784T>C		intron	N/A	ENSP00000414188.3

Frequencies

GnomAD3 genomes AF: 0.561 AC: 85138 AN: 151858 Hom.: 24660 Cov.: 32

Gnomad AFR AF: 0.699

Gnomad AMI AF: 0.515

Gnomad AMR AF: 0.535

Gnomad ASJ AF: 0.580

Gnomad EAS AF: 0.248

Gnomad SAS AF: 0.503

Gnomad FIN AF: 0.529

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.514

Gnomad OTH AF: 0.579

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

GnomAD4 genome AF: 0.561 AC: 85214 AN: 151976 Hom.: 24683 Cov.: 32 AF XY: 0.558 AC XY: 41499 AN XY: 74308

African (AFR) AF: 0.699 AC: 28986 AN: 41450

American (AMR) AF: 0.535 AC: 8168 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.580 AC: 2013 AN: 3472

East Asian (EAS) AF: 0.247 AC: 1279 AN: 5170

South Asian (SAS) AF: 0.502 AC: 2421 AN: 4818

European-Finnish (FIN) AF: 0.529 AC: 5578 AN: 10550

Middle Eastern (MID) AF: 0.545 AC: 159 AN: 292

European-Non Finnish (NFE) AF: 0.514 AC: 34922 AN: 67930

Other (OTH) AF: 0.579 AC: 1219 AN: 2104

Alfa AF: 0.526 Hom.: 11391

Bravo AF: 0.564

Asia WGS AF: 0.460 AC: 1601 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.0
DANN	Benign	0.23
PhyloP100		-0.81
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: rs2654879; hg19: chr1-242600606; COSMIC: COSV59161655;