rs6816483

Variant names:

• chr4-765945-T-C
• rs6816483
• NM_006315.7:c.682-87T>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.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
• Publications: 8 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]

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

LOC124900163 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
PCGF3	NM_006315.7	c.682-87T>C		intron_variant	Intron 10 of 10	ENST00000362003.10	NP_006306.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PCGF3	ENST00000362003.10	c.682-87T>C		intron_variant	Intron 10 of 10	5	NM_006315.7	ENSP00000354724.5

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

African (AFR) AF: 0.714 AC: 18854 AN: 26406

American (AMR) AF: 0.554 AC: 24203 AN: 43662

Ashkenazi Jewish (ASJ) AF: 0.779 AC: 17835 AN: 22892

East Asian (EAS) AF: 0.551 AC: 20846 AN: 37820

South Asian (SAS) AF: 0.765 AC: 58901 AN: 76992

European-Finnish (FIN) AF: 0.644 AC: 32410 AN: 50304

Middle Eastern (MID) AF: 0.818 AC: 4060 AN: 4962

European-Non Finnish (NFE) AF: 0.682 AC: 522482 AN: 766542

Other (OTH) AF: 0.693 AC: 32995 AN: 47582

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

African (AFR) AF: 0.711 AC: 29477 AN: 41478

American (AMR) AF: 0.611 AC: 9347 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.792 AC: 2749 AN: 3470

East Asian (EAS) AF: 0.568 AC: 2936 AN: 5168

South Asian (SAS) AF: 0.745 AC: 3593 AN: 4824

European-Finnish (FIN) AF: 0.654 AC: 6927 AN: 10584

Middle Eastern (MID) AF: 0.844 AC: 248 AN: 294

European-Non Finnish (NFE) AF: 0.685 AC: 46588 AN: 67964

Other (OTH) AF: 0.714 AC: 1506 AN: 2108

Alfa AF: 0.671 Hom.: 4543

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
PhyloP100		-1.3
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.2
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: rs6816483; hg19: chr4-759733; COSMIC: COSV62858530; COSMIC: COSV62858530;