rs9332466

Variant names:

• chr4-750310-T-C
• rs9332466
• NM_006315.7:c.462+5622T>C

Variant summary

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

The NM_006315.7(PCGF3):​c.462+5622T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.23 in 152,180 control chromosomes in the GnomAD database, including 4,626 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 0.23 (4626 hom., cov: 33)
• Consequence: PCGF3 NM_006315.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.801
• Publications: 11 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]

LOC124900163 (HGNC:):

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 (AMR) allele frequency at 95% confidence interval = 0.335 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.462+5622T>C		intron	N/A	NP_006306.2
	PCGF3	NM_001317836.3		c.462+5622T>C		intron	N/A	NP_001304765.1
	PCGF3	NM_001395245.1		c.462+5622T>C		intron	N/A	NP_001382174.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PCGF3	ENST00000362003.10	TSL:5 MANE Select	c.462+5622T>C		intron	N/A	ENSP00000354724.5
	PCGF3	ENST00000470161.6	TSL:1	c.462+5622T>C		intron	N/A	ENSP00000420489.2
	PCGF3	ENST00000870362.1		c.462+5622T>C		intron	N/A	ENSP00000540421.1

Frequencies

GnomAD3 genomes AF: 0.230 AC: 34906 AN: 152062 Hom.: 4612 Cov.: 33

Gnomad AFR AF: 0.139

Gnomad AMI AF: 0.143

Gnomad AMR AF: 0.341

Gnomad ASJ AF: 0.135

Gnomad EAS AF: 0.326

Gnomad SAS AF: 0.0841

Gnomad FIN AF: 0.263

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.265

Gnomad OTH AF: 0.219

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

GnomAD4 genome AF: 0.230 AC: 34955 AN: 152180 Hom.: 4626 Cov.: 33 AF XY: 0.230 AC XY: 17138 AN XY: 74394

African (AFR) AF: 0.139 AC: 5781 AN: 41556

American (AMR) AF: 0.342 AC: 5227 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.135 AC: 470 AN: 3472

East Asian (EAS) AF: 0.326 AC: 1687 AN: 5168

South Asian (SAS) AF: 0.0842 AC: 406 AN: 4824

European-Finnish (FIN) AF: 0.263 AC: 2785 AN: 10584

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.264 AC: 17981 AN: 67984

Other (OTH) AF: 0.219 AC: 463 AN: 2116

Alfa AF: 0.249 Hom.: 13819

Bravo AF: 0.234

Asia WGS AF: 0.185 AC: 643 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.9
DANN	Benign	0.69
PhyloP100		0.80
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: rs9332466; hg19: chr4-744098;