21-45842476-G-A

Position:

• chr21-45842476-G-A

Variant summary

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

The NM_001384156.1(PCBP3):​c.-125-7485G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.827 in 152,188 control chromosomes in the GnomAD database, including 52,329 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 0.83 (52329 hom., cov: 33)
• Consequence: PCBP3 NM_001384156.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11

Genes affected

PCBP3 (HGNC:8651): (poly(rC) binding protein 3) This gene encodes a member of the KH-domain protein subfamily. Proteins of this subfamily, also referred to as alpha-CPs, bind to RNA with a specificity for C-rich pyrimidine regions. Alpha-CPs play important roles in post-transcriptional activities and have different cellular distributions. The protein encoded by this gene lacks the nuclear localization signals found in other subfamily members. Alternative splicing results in multiple transcript variants encoding distinct isoforms. [provided by RefSeq, Jan 2017]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.911 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PCBP3	NM_001384156.1	c.-125-7485G>A		intron_variant		ENST00000681687.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PCBP3	ENST00000681687.1	c.-125-7485G>A		intron_variant			NM_001384156.1	P4
PCBP3	ENST00000400314.5	c.-125-7485G>A		intron_variant		5		P4

Frequencies

GnomAD3 genomes AF: 0.827 AC: 125805 AN: 152070 Hom.: 52297 Cov.: 33

Gnomad AFR AF: 0.738

Gnomad AMI AF: 0.894

Gnomad AMR AF: 0.844

Gnomad ASJ AF: 0.838

Gnomad EAS AF: 0.934

Gnomad SAS AF: 0.910

Gnomad FIN AF: 0.903

Gnomad MID AF: 0.858

Gnomad NFE AF: 0.850

Gnomad OTH AF: 0.840

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

GnomAD4 genome AF: 0.827 AC: 125886 AN: 152188 Hom.: 52329 Cov.: 33 AF XY: 0.830 AC XY: 61760 AN XY: 74420

Gnomad4 AFR AF: 0.737

Gnomad4 AMR AF: 0.844

Gnomad4 ASJ AF: 0.838

Gnomad4 EAS AF: 0.933

Gnomad4 SAS AF: 0.911

Gnomad4 FIN AF: 0.903

Gnomad4 NFE AF: 0.850

Gnomad4 OTH AF: 0.842

Alfa AF: 0.848 Hom.: 24945

Bravo AF: 0.817

Asia WGS AF: 0.911 AC: 3170 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.1
DANN	Benign	0.34

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: rs2330247; hg19: chr21-47262390;