12-14507250-T-C

Variant names:

• chr12-14507250-T-C
• rs3827886
• NM_024829.6:c.1187-132A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024829.6. 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
	PLBD1	NM_024829.6	MANE Select	c.1187-132A>G		intron	N/A	NP_079105.4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PLBD1	ENST00000240617.10	TSL:1 MANE Select	c.1187-132A>G		intron	N/A	ENSP00000240617.5	Q6P4A8
	PLBD1	ENST00000918098.1		c.1346-132A>G		intron	N/A	ENSP00000588157.1
	PLBD1	ENST00000945093.1		c.1184-132A>G		intron	N/A	ENSP00000615152.1

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

African (AFR) AF: 0.0351 AC: 521 AN: 14838

American (AMR) AF: 0.0818 AC: 1550 AN: 18938

Ashkenazi Jewish (ASJ) AF: 0.147 AC: 2049 AN: 13980

East Asian (EAS) AF: 0.112 AC: 3726 AN: 33342

South Asian (SAS) AF: 0.204 AC: 8539 AN: 41790

European-Finnish (FIN) AF: 0.151 AC: 5741 AN: 38028

Middle Eastern (MID) AF: 0.0951 AC: 217 AN: 2282

European-Non Finnish (NFE) AF: 0.138 AC: 49753 AN: 359822

Other (OTH) AF: 0.134 AC: 3892 AN: 29114

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

African (AFR) AF: 0.0347 AC: 1442 AN: 41578

American (AMR) AF: 0.0933 AC: 1424 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.169 AC: 587 AN: 3472

East Asian (EAS) AF: 0.0941 AC: 488 AN: 5188

South Asian (SAS) AF: 0.210 AC: 1014 AN: 4826

European-Finnish (FIN) AF: 0.158 AC: 1671 AN: 10598

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.140 AC: 9511 AN: 68022

Other (OTH) AF: 0.117 AC: 247 AN: 2114

Alfa AF: 0.126 Hom.: 2853

Bravo AF: 0.0993

Asia WGS AF: 0.182 AC: 637 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.57
DANN	Benign	0.70
PhyloP100		-0.093
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs3827886; hg19: chr12-14660184;