rs2898002

Variant names:

• chr12-47082444-C-G
• rs2898002
• NM_138371.3:c.-609+2719C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_138371.3(PCED1B):​c.-609+2719C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.274 in 152,096 control chromosomes in the GnomAD database, including 6,236 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 0.27 (6236 hom., cov: 32)
• Consequence: PCED1B NM_138371.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.37
• Publications: 5 publications found

Genes affected

PCED1B (HGNC:28255): (PC-esterase domain containing 1B) This gene encodes a protein that belongs to the GDSL/SGNH-like acyl-esterase family. Members of this family are hydrolases thought to function in modification of biopolymers on the cell surface. Alternate splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jul 2013]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.381 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PCED1B	NM_138371.3	c.-609+2719C>G		intron_variant	Intron 1 of 3	ENST00000546455.6	NP_612380.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PCED1B	ENST00000546455.6	c.-609+2719C>G		intron_variant	Intron 1 of 3	1	NM_138371.3	ENSP00000446688.1
PCED1B	ENST00000432328.2	c.-141+2719C>G		intron_variant	Intron 1 of 2	3		ENSP00000396040.1

Frequencies

GnomAD3 genomes AF: 0.274 AC: 41689 AN: 151978 Hom.: 6229 Cov.: 32

Gnomad AFR AF: 0.167

Gnomad AMI AF: 0.198

Gnomad AMR AF: 0.388

Gnomad ASJ AF: 0.280

Gnomad EAS AF: 0.292

Gnomad SAS AF: 0.393

Gnomad FIN AF: 0.317

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.299

Gnomad OTH AF: 0.282

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

GnomAD4 genome AF: 0.274 AC: 41722 AN: 152096 Hom.: 6236 Cov.: 32 AF XY: 0.278 AC XY: 20647 AN XY: 74332

African (AFR) AF: 0.167 AC: 6921 AN: 41526

American (AMR) AF: 0.389 AC: 5944 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.280 AC: 971 AN: 3470

East Asian (EAS) AF: 0.293 AC: 1510 AN: 5162

South Asian (SAS) AF: 0.392 AC: 1889 AN: 4818

European-Finnish (FIN) AF: 0.317 AC: 3348 AN: 10552

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.299 AC: 20300 AN: 67972

Other (OTH) AF: 0.283 AC: 595 AN: 2106

Alfa AF: 0.287 Hom.: 908

Bravo AF: 0.274

Asia WGS AF: 0.344 AC: 1195 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	15
DANN	Benign	0.85
PhyloP100		2.4
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: rs2898002; hg19: chr12-47476227;