rs13138362

Variant names:

• chr4-763198-T-C
• rs13138362
• NM_006315.7:c.600+1782T>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.600+1782T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.328 in 152,056 control chromosomes in the GnomAD database, including 9,569 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 0.33 (9569 hom., cov: 32)
• Consequence: PCGF3 NM_006315.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.584
• Publications: 5 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]

LOC124900163 (HGNC:):

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.528 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006315.7. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PCGF3	NM_006315.7	MANE Select	c.600+1782T>C		intron	N/A	NP_006306.2
	PCGF3	NM_001317836.3		c.600+1782T>C		intron	N/A	NP_001304765.1	Q3KNV8-1
	PCGF3	NM_001395245.1		c.600+1782T>C		intron	N/A	NP_001382174.1	Q3KNV8-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PCGF3	ENST00000362003.10	TSL:5 MANE Select	c.600+1782T>C		intron	N/A	ENSP00000354724.5	Q3KNV8-1
	PCGF3	ENST00000470161.6	TSL:1	c.600+1782T>C		intron	N/A	ENSP00000420489.2	Q3KNV8-1
	PCGF3	ENST00000870362.1		c.600+1782T>C		intron	N/A	ENSP00000540421.1

Frequencies

GnomAD3 genomes AF: 0.328 AC: 49766 AN: 151938 Hom.: 9566 Cov.: 32

Gnomad AFR AF: 0.534

Gnomad AMI AF: 0.259

Gnomad AMR AF: 0.239

Gnomad ASJ AF: 0.221

Gnomad EAS AF: 0.180

Gnomad SAS AF: 0.275

Gnomad FIN AF: 0.261

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.254

Gnomad OTH AF: 0.310

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

GnomAD4 genome AF: 0.328 AC: 49799 AN: 152056 Hom.: 9569 Cov.: 32 AF XY: 0.325 AC XY: 24183 AN XY: 74346

African (AFR) AF: 0.534 AC: 22110 AN: 41432

American (AMR) AF: 0.239 AC: 3653 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.221 AC: 769 AN: 3472

East Asian (EAS) AF: 0.181 AC: 935 AN: 5176

South Asian (SAS) AF: 0.277 AC: 1332 AN: 4812

European-Finnish (FIN) AF: 0.261 AC: 2763 AN: 10576

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.254 AC: 17270 AN: 67980

Other (OTH) AF: 0.307 AC: 649 AN: 2112

Alfa AF: 0.280 Hom.: 17599

Bravo AF: 0.334

Asia WGS AF: 0.234 AC: 813 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	11
DANN	Benign	0.77
PhyloP100		0.58
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: rs13138362; hg19: chr4-756986;