12-47214352-G-C

Position:

• chr12-47214352-G-C

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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/exons	MANE	UniProt
PCED1B	NM_138371.3	c.-525-1870G>C		intron_variant		ENST00000546455.6
PCED1B-AS1	NR_026544.1	n.160+1813C>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PCED1B	ENST00000546455.6	c.-525-1870G>C		intron_variant		1	NM_138371.3	P1
PCED1B-AS1	ENST00000697435.1	n.204+1813C>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.0822

Gnomad4 AMR AF: 0.161

Gnomad4 ASJ AF: 0.241

Gnomad4 EAS AF: 0.0526

Gnomad4 SAS AF: 0.0989

Gnomad4 FIN AF: 0.259

Gnomad4 NFE AF: 0.281

Gnomad4 OTH AF: 0.196

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

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: rs2111903; hg19: chr12-47608135;