rs1898153

Positions:

• chr1-242129492-C-T

Variant summary

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

The NM_001372062.1(PLD5):​c.736-4827G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.384 in 152,014 control chromosomes in the GnomAD database, including 11,994 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 0.38 (11994 hom., cov: 33)
• Consequence: PLD5 NM_001372062.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.236

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=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.592 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PLD5	NM_001372062.1	c.736-4827G>A		intron_variant		ENST00000536534.7	NP_001358991.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PLD5	ENST00000536534.7	c.736-4827G>A		intron_variant		1	NM_001372062.1	ENSP00000440896.1

Frequencies

GnomAD3 genomes AF: 0.385 AC: 58417 AN: 151898 Hom.: 11989 Cov.: 33

Gnomad AFR AF: 0.258

Gnomad AMI AF: 0.411

Gnomad AMR AF: 0.472

Gnomad ASJ AF: 0.342

Gnomad EAS AF: 0.610

Gnomad SAS AF: 0.485

Gnomad FIN AF: 0.435

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.411

Gnomad OTH AF: 0.397

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

GnomAD4 genome AF: 0.384 AC: 58444 AN: 152014 Hom.: 11994 Cov.: 33 AF XY: 0.388 AC XY: 28804 AN XY: 74290

Gnomad4 AFR AF: 0.258

Gnomad4 AMR AF: 0.472

Gnomad4 ASJ AF: 0.342

Gnomad4 EAS AF: 0.610

Gnomad4 SAS AF: 0.485

Gnomad4 FIN AF: 0.435

Gnomad4 NFE AF: 0.411

Gnomad4 OTH AF: 0.398

Alfa AF: 0.392 Hom.: 2077

Bravo AF: 0.382

Asia WGS AF: 0.518 AC: 1802 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.6
DANN	Benign	0.79

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: rs1898153; hg19: chr1-242292794;