rs2111903

Variant names:

• chr12-47214352-G-C
• rs2111903
• NM_138371.3:c.-525-1870G>C

Your query was ambiguous. Multiple possible variants found:

• chr12-47214352-G-C
• chr12-47214352-G-T

Variant summary

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

The NM_138371.3(PCED1B):​c.-525-1870G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.197 in 152,134 control chromosomes in the GnomAD database, including 3,639 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 0.20 (3639 hom., cov: 32)
• Consequence: PCED1B NM_138371.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.290
• Publications: 2 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]

PCED1B-AS1 (HGNC:44166): (PCED1B antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.278 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PCED1B	NM_138371.3	c.-525-1870G>C		intron_variant	Intron 2 of 3	ENST00000546455.6	NP_612380.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PCED1B	ENST00000546455.6	c.-525-1870G>C		intron_variant	Intron 2 of 3	1	NM_138371.3	ENSP00000446688.1

Frequencies

GnomAD3 genomes AF: 0.197 AC: 29904 AN: 152016 Hom.: 3639 Cov.: 32

Gnomad AFR AF: 0.0822

Gnomad AMI AF: 0.154

Gnomad AMR AF: 0.161

Gnomad ASJ AF: 0.241

Gnomad EAS AF: 0.0527

Gnomad SAS AF: 0.0980

Gnomad FIN AF: 0.259

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.281

Gnomad OTH AF: 0.199

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

GnomAD4 genome AF: 0.197 AC: 29907 AN: 152134 Hom.: 3639 Cov.: 32 AF XY: 0.191 AC XY: 14207 AN XY: 74352

African (AFR) AF: 0.0822 AC: 3412 AN: 41514

American (AMR) AF: 0.161 AC: 2457 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.241 AC: 837 AN: 3470

East Asian (EAS) AF: 0.0526 AC: 273 AN: 5186

South Asian (SAS) AF: 0.0989 AC: 477 AN: 4824

European-Finnish (FIN) AF: 0.259 AC: 2739 AN: 10562

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.281 AC: 19106 AN: 67976

Other (OTH) AF: 0.196 AC: 415 AN: 2112

Alfa AF: 0.222 Hom.: 554

Bravo AF: 0.183

Asia WGS AF: 0.0750 AC: 265 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.14
DANN	Benign	0.68
PhyloP100		0.29
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: rs2111903; hg19: chr12-47608135;