rs4690296

Positions:

• chr4-738473-A-G

Variant summary

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

The NM_006315.7(PCGF3):​c.262+952A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0777 in 152,272 control chromosomes in the GnomAD database, including 509 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 0.078 (509 hom., cov: 33)
• Consequence: PCGF3 NM_006315.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.183

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.135 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PCGF3	NM_006315.7	c.262+952A>G		intron_variant		ENST00000362003.10	NP_006306.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PCGF3	ENST00000362003.10	c.262+952A>G		intron_variant		5	NM_006315.7	ENSP00000354724	P1

Frequencies

GnomAD3 genomes AF: 0.0778 AC: 11841 AN: 152154 Hom.: 511 Cov.: 33

Gnomad AFR AF: 0.0505

Gnomad AMI AF: 0.0505

Gnomad AMR AF: 0.0795

Gnomad ASJ AF: 0.0902

Gnomad EAS AF: 0.0519

Gnomad SAS AF: 0.145

Gnomad FIN AF: 0.105

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0869

Gnomad OTH AF: 0.0707

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

GnomAD4 genome AF: 0.0777 AC: 11839 AN: 152272 Hom.: 509 Cov.: 33 AF XY: 0.0813 AC XY: 6050 AN XY: 74454

Gnomad4 AFR AF: 0.0505

Gnomad4 AMR AF: 0.0793

Gnomad4 ASJ AF: 0.0902

Gnomad4 EAS AF: 0.0520

Gnomad4 SAS AF: 0.144

Gnomad4 FIN AF: 0.105

Gnomad4 NFE AF: 0.0869

Gnomad4 OTH AF: 0.0714

Alfa AF: 0.0875 Hom.: 922

Bravo AF: 0.0721

Asia WGS AF: 0.112 AC: 390 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	2.6
DANN	Benign	0.35

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: rs4690296; hg19: chr4-732261;