rs3827886

Positions:

• chr12-14507250-T-C

Variant summary

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

The NM_024829.6(PLBD1):​c.1187-132A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.132 in 704,406 control chromosomes in the GnomAD database, including 6,836 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 0.11 (1180 hom., cov: 33)
  • Exomes 𝑓: 0.14 (5656 hom.)
• Consequence: PLBD1 NM_024829.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0930

Genes affected

PLBD1 (HGNC:26215): (phospholipase B domain containing 1) Predicted to enable phospholipase activity. Predicted to be involved in phospholipid catabolic process. Located in extracellular space. [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 (SAS) allele frequency at 95% confidence interval = 0.199 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PLBD1	NM_024829.6	c.1187-132A>G		intron_variant		ENST00000240617.10	NP_079105.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PLBD1	ENST00000240617.10	c.1187-132A>G		intron_variant		1	NM_024829.6	ENSP00000240617	P1

Frequencies

GnomAD3 genomes AF: 0.110 AC: 16705 AN: 152154 Hom.: 1179 Cov.: 33

Gnomad AFR AF: 0.0347

Gnomad AMI AF: 0.332

Gnomad AMR AF: 0.0935

Gnomad ASJ AF: 0.169

Gnomad EAS AF: 0.0938

Gnomad SAS AF: 0.210

Gnomad FIN AF: 0.158

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.140

Gnomad OTH AF: 0.112

GnomAD4 exome AF: 0.138 AC: 75988 AN: 552134 Hom.: 5656 AF XY: 0.141 AC XY: 40143 AN XY: 285598

Gnomad4 AFR exome AF: 0.0351

Gnomad4 AMR exome AF: 0.0818

Gnomad4 ASJ exome AF: 0.147

Gnomad4 EAS exome AF: 0.112

Gnomad4 SAS exome AF: 0.204

Gnomad4 FIN exome AF: 0.151

Gnomad4 NFE exome AF: 0.138

Gnomad4 OTH exome AF: 0.134

GnomAD4 genome AF: 0.110 AC: 16716 AN: 152272 Hom.: 1180 Cov.: 33 AF XY: 0.112 AC XY: 8327 AN XY: 74466

Gnomad4 AFR AF: 0.0347

Gnomad4 AMR AF: 0.0933

Gnomad4 ASJ AF: 0.169

Gnomad4 EAS AF: 0.0941

Gnomad4 SAS AF: 0.210

Gnomad4 FIN AF: 0.158

Gnomad4 NFE AF: 0.140

Gnomad4 OTH AF: 0.117

Alfa AF: 0.134 Hom.: 2068

Bravo AF: 0.0993

Asia WGS AF: 0.182 AC: 637 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	0.57
DANN	Benign	0.70

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs3827886; hg19: chr12-14660184;