rs2839037

Variant names:

• chr21-45892549-G-A
• rs2839037
• NM_001384156.1:c.11-3659G>A

Your query was ambiguous. Multiple possible variants found:

• chr21-45892549-G-A
• chr21-45892549-G-C
• chr21-45892549-G-T

Variant summary

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

The NM_001384156.1(PCBP3):​c.11-3659G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.452 in 142,736 control chromosomes in the GnomAD database, including 16,950 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 0.45 (16950 hom., cov: 27)
• Consequence: PCBP3 NM_001384156.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.203
• Publications: 0 publications found

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

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.68 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001384156.1. 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
	PCBP3	NM_001384156.1	MANE Select	c.11-3659G>A		intron	N/A	NP_001371085.1	P57721-1
	PCBP3	NM_001348240.2		c.11-3659G>A		intron	N/A	NP_001335169.1
	PCBP3	NM_001382279.1		c.11-3659G>A		intron	N/A	NP_001369208.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PCBP3	ENST00000681687.1	MANE Select	c.11-3659G>A		intron	N/A	ENSP00000505796.1	P57721-1
	PCBP3	ENST00000400308.5	TSL:1	c.11-3659G>A		intron	N/A	ENSP00000383163.1	P57721-2
	PCBP3	ENST00000400314.5	TSL:5	c.11-3659G>A		intron	N/A	ENSP00000383168.1	P57721-1

Frequencies

GnomAD3 genomes AF: 0.452 AC: 64511 AN: 142628 Hom.: 16915 Cov.: 27

Gnomad AFR AF: 0.686

Gnomad AMI AF: 0.346

Gnomad AMR AF: 0.384

Gnomad ASJ AF: 0.404

Gnomad EAS AF: 0.298

Gnomad SAS AF: 0.367

Gnomad FIN AF: 0.306

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.371

Gnomad OTH AF: 0.425

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

GnomAD4 genome AF: 0.452 AC: 64581 AN: 142736 Hom.: 16950 Cov.: 27 AF XY: 0.446 AC XY: 30940 AN XY: 69434

African (AFR) AF: 0.687 AC: 26517 AN: 38614

American (AMR) AF: 0.383 AC: 5538 AN: 14446

Ashkenazi Jewish (ASJ) AF: 0.404 AC: 1340 AN: 3320

East Asian (EAS) AF: 0.298 AC: 1429 AN: 4798

South Asian (SAS) AF: 0.365 AC: 1566 AN: 4290

European-Finnish (FIN) AF: 0.306 AC: 2999 AN: 9792

Middle Eastern (MID) AF: 0.571 AC: 161 AN: 282

European-Non Finnish (NFE) AF: 0.371 AC: 23917 AN: 64404

Other (OTH) AF: 0.422 AC: 823 AN: 1948

Alfa AF: 0.413 Hom.: 17221

Bravo AF: 0.477

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.7
DANN	Benign	0.64
PhyloP100		0.20
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: rs2839037; hg19: chr21-47312463; COSMIC: COSV68407194; COSMIC: COSV68407194;