rs4234853

Positions:

• chr4-741362-G-A

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PCGF3	NM_006315.7	c.263-2112G>A		intron_variant		ENST00000362003.10
LOC107986246	XR_001741543.2	n.1174G>A		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PCGF3	ENST00000362003.10	c.263-2112G>A		intron_variant		5	NM_006315.7	P1

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

Gnomad4 AFR AF: 0.0911

Gnomad4 AMR AF: 0.203

Gnomad4 ASJ AF: 0.344

Gnomad4 EAS AF: 0.201

Gnomad4 SAS AF: 0.267

Gnomad4 FIN AF: 0.201

Gnomad4 NFE AF: 0.261

Gnomad4 OTH AF: 0.228

Alfa AF: 0.259 Hom.: 9140

Bravo AF: 0.201

Asia WGS AF: 0.207 AC: 719 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.4
DANN	Benign	0.58

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: rs4234853; hg19: chr4-735150;