rs9332466

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PCGF3	NM_006315.7	c.462+5622T>C		intron_variant	Intron 8 of 10	ENST00000362003.10	NP_006306.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PCGF3	ENST00000362003.10	c.462+5622T>C		intron_variant	Intron 8 of 10	5	NM_006315.7	ENSP00000354724.5

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

Gnomad4 AFR AF: 0.139

Gnomad4 AMR AF: 0.342

Gnomad4 ASJ AF: 0.135

Gnomad4 EAS AF: 0.326

Gnomad4 SAS AF: 0.0842

Gnomad4 FIN AF: 0.263

Gnomad4 NFE AF: 0.264

Gnomad4 OTH AF: 0.219

Alfa AF: 0.251 Hom.: 9667

Bravo AF: 0.234

Asia WGS AF: 0.185 AC: 643 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.9
DANN	Benign	0.69

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: rs9332466; hg19: chr4-744098;