rs1439523

Positions:

• chr1-242368352-T-C
• chr1-242368352-T-G

Variant summary

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

The NM_001372062.1(PLD5):​c.190-20110A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.895 in 152,138 control chromosomes in the GnomAD database, including 62,112 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 0.90 (62112 hom., cov: 32)
• Consequence: PLD5 NM_001372062.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.928

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=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.974 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PLD5	NM_001372062.1	c.190-20110A>G		intron_variant		ENST00000536534.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PLD5	ENST00000536534.7	c.190-20110A>G		intron_variant		1	NM_001372062.1	P1

Frequencies

GnomAD3 genomes AF: 0.896 AC: 136169 AN: 152020 Hom.: 62112 Cov.: 32

Gnomad AFR AF: 0.705

Gnomad AMI AF: 0.984

Gnomad AMR AF: 0.932

Gnomad ASJ AF: 0.921

Gnomad EAS AF: 0.910

Gnomad SAS AF: 0.943

Gnomad FIN AF: 0.995

Gnomad MID AF: 0.940

Gnomad NFE AF: 0.980

Gnomad OTH AF: 0.911

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

GnomAD4 genome AF: 0.895 AC: 136204 AN: 152138 Hom.: 62112 Cov.: 32 AF XY: 0.897 AC XY: 66713 AN XY: 74368

Gnomad4 AFR AF: 0.704

Gnomad4 AMR AF: 0.932

Gnomad4 ASJ AF: 0.921

Gnomad4 EAS AF: 0.910

Gnomad4 SAS AF: 0.942

Gnomad4 FIN AF: 0.995

Gnomad4 NFE AF: 0.980

Gnomad4 OTH AF: 0.911

Alfa AF: 0.953 Hom.: 69154

Bravo AF: 0.881

Asia WGS AF: 0.873 AC: 3037 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.5
DANN	Benign	0.34

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: rs1439523; hg19: chr1-242531654;