rs4234853

Variant names:

• chr4-741362-G-A
• rs4234853
• NM_006315.7:c.263-2112G>A

Variant summary

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

The NM_006315.7(PCGF3):​c.263-2112G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.204 in 152,212 control chromosomes in the GnomAD database, including 3,694 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 (3694 hom., cov: 33)
• Consequence: PCGF3 NM_006315.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0380
• Publications: 21 publications found

Genes affected

PCGF3 (HGNC:10066): (polycomb group ring finger 3) The protein encoded by this gene contains a C3HC4 type RING finger, which is a motif known to be involved in protein-protein interactions. The specific function of this protein has not yet been determined. [provided by RefSeq, Jul 2008]

LOC107986246 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.258 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006315.7. 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
	PCGF3	NM_006315.7	MANE Select	c.263-2112G>A		intron	N/A	NP_006306.2
	PCGF3	NM_001317836.3		c.263-2112G>A		intron	N/A	NP_001304765.1	Q3KNV8-1
	PCGF3	NM_001395245.1		c.263-2112G>A		intron	N/A	NP_001382174.1	Q3KNV8-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PCGF3	ENST00000362003.10	TSL:5 MANE Select	c.263-2112G>A		intron	N/A	ENSP00000354724.5	Q3KNV8-1
	PCGF3	ENST00000470161.6	TSL:1	c.263-2112G>A		intron	N/A	ENSP00000420489.2	Q3KNV8-1
	PCGF3	ENST00000870362.1		c.263-2112G>A		intron	N/A	ENSP00000540421.1

Frequencies

GnomAD3 genomes AF: 0.204 AC: 31088 AN: 152094 Hom.: 3693 Cov.: 33

Gnomad AFR AF: 0.0911

Gnomad AMI AF: 0.258

Gnomad AMR AF: 0.203

Gnomad ASJ AF: 0.344

Gnomad EAS AF: 0.200

Gnomad SAS AF: 0.266

Gnomad FIN AF: 0.201

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.261

Gnomad OTH AF: 0.232

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

GnomAD4 genome AF: 0.204 AC: 31090 AN: 152212 Hom.: 3694 Cov.: 33 AF XY: 0.201 AC XY: 14958 AN XY: 74418

African (AFR) AF: 0.0911 AC: 3783 AN: 41546

American (AMR) AF: 0.203 AC: 3103 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.344 AC: 1193 AN: 3470

East Asian (EAS) AF: 0.201 AC: 1041 AN: 5188

South Asian (SAS) AF: 0.267 AC: 1290 AN: 4828

European-Finnish (FIN) AF: 0.201 AC: 2131 AN: 10592

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.261 AC: 17752 AN: 67986

Other (OTH) AF: 0.228 AC: 482 AN: 2112

Alfa AF: 0.245 Hom.: 14871

Bravo AF: 0.201

Asia WGS AF: 0.207 AC: 719 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.4
DANN	Benign	0.58
PhyloP100		-0.038
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: rs4234853; hg19: chr4-735150;