rs6816483

chr4-765945-T-C

Variant summary

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

The NM_006315.7(PCGF3):c.682-87T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.681 in 1,229,256 control chromosomes in the GnomAD database, including 286,969 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 0.68 (35974 hom., cov: 33)
  • Exomes 𝑓: 0.68 (250995 hom.)
• Consequence: PCGF3 NM_006315.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.31

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:):

PCGF3-AS1 (HGNC:56108): (PCGF3 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.724 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PCGF3	NM_006315.7	c.682-87T>C		intron_variant		ENST00000362003.10
LOC124900163	XM_047416474.1	c.-2693-3205A>G		intron_variant
PCGF3-AS1	NR_171661.1	n.79-898A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PCGF3	ENST00000362003.10	c.682-87T>C		intron_variant		5	NM_006315.7	P1
PCGF3-AS1	ENST00000660016.1	n.79-3205A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.684 AC: 104027 AN: 151976 Hom.: 35947 Cov.: 33

Gnomad AFR AF: 0.711

Gnomad AMI AF: 0.801

Gnomad AMR AF: 0.612

Gnomad ASJ AF: 0.792

Gnomad EAS AF: 0.568

Gnomad SAS AF: 0.744

Gnomad FIN AF: 0.654

Gnomad MID AF: 0.848

Gnomad NFE AF: 0.685

Gnomad OTH AF: 0.714

GnomAD4 exome AF: 0.680 AC: 732586 AN: 1077162 Hom.: 250995 AF XY: 0.685 AC XY: 377955 AN XY: 551618

Gnomad4 AFR exome AF: 0.714

Gnomad4 AMR exome AF: 0.554

Gnomad4 ASJ exome AF: 0.779

Gnomad4 EAS exome AF: 0.551

Gnomad4 SAS exome AF: 0.765

Gnomad4 FIN exome AF: 0.644

Gnomad4 NFE exome AF: 0.682

Gnomad4 OTH exome AF: 0.693

GnomAD4 genome AF: 0.684 AC: 104100 AN: 152094 Hom.: 35974 Cov.: 33 AF XY: 0.682 AC XY: 50721 AN XY: 74332

Gnomad4 AFR AF: 0.711

Gnomad4 AMR AF: 0.611

Gnomad4 ASJ AF: 0.792

Gnomad4 EAS AF: 0.568

Gnomad4 SAS AF: 0.745

Gnomad4 FIN AF: 0.654

Gnomad4 NFE AF: 0.685

Gnomad4 OTH AF: 0.714

Alfa AF: 0.670 Hom.: 4332

Bravo AF: 0.684

Asia WGS AF: 0.657 AC: 2286 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	0.71
Dann	Benign	0.28
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.2

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: rs6816483; hg19: chr4-759733; COSMIC: COSV62858530; COSMIC: COSV62858530;