Genetic Variant NM_006315.7:c.525C>T (chr4-761341-C-T) – ACMG Classification: Benign (-11 pts)

Variant summary

Our verdict is Benign. The variant received -11 ACMG points: 0P and 11B. BP4_ModerateBP7BA1

The NM_006315.7(PCGF3):c.525C>T(p.Arg175Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0598 in 1,610,694 control chromosomes in the GnomAD database, including 3,446 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 0.051 ( 286 hom., cov: 33)

Exomes 𝑓: 0.061 ( 3160 hom. )

Consequence

PCGF3
NM_006315.7 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.01

Publications

15 publications found

Variant links:

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 links:

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

PCGF3-AS1 links:

LOC124900163 (HGNC:):

LOC124900163 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.46).

BP7

Synonymous conserved (PhyloP=1.01 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.114 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PCGF3	NM_006315.7 link	c.525C>T	p.Arg175Arg	synonymous_variant	Exon 9 of 11	ENST00000362003.10	NP_006306.2	Q3KNV8-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PCGF3	ENST00000362003.10 link	c.525C>T	p.Arg175Arg	synonymous_variant	Exon 9 of 11	5	NM_006315.7	ENSP00000354724.5		Q3KNV8-1

Frequencies

GnomAD3 genomes

AF:

0.0511

AC:

7786

AN:

152220

Hom.:

286

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0161

Gnomad AMI

AF:

0.139

Gnomad AMR

AF:

0.0613

Gnomad ASJ

AF:

0.130

Gnomad EAS

AF:

0.122

Gnomad SAS

AF:

0.0576

Gnomad FIN

AF:

0.0604

Gnomad MID

AF:

0.0601

Gnomad NFE

AF:

0.0572

Gnomad OTH

AF:

0.0654

GnomAD2 exomes

AF:

0.0643

AC:

15911

AN:

247314

AF XY:

0.0649

show subpopulations

Gnomad AFR exome

AF:

0.0150

Gnomad AMR exome

AF:

0.0620

Gnomad ASJ exome

AF:

0.136

Gnomad EAS exome

AF:

0.118

Gnomad FIN exome

AF:

0.0698

Gnomad NFE exome

AF:

0.0562

Gnomad OTH exome

AF:

0.0703

GnomAD4 exome

AF:

0.0607

AC:

88554

AN:

1458356

Hom.:

3160

Cov.:

AF XY:

0.0609

AC XY:

44157

AN XY:

725046

show subpopulations

African (AFR)

AF:

0.0143

AC:

476

AN:

33390

American (AMR)

AF:

0.0636

AC:

2819

AN:

44292

Ashkenazi Jewish (ASJ)

AF:

0.134

AC:

3500

AN:

26070

East Asian (EAS)

AF:

0.148

AC:

5863

AN:

39566

South Asian (SAS)

AF:

0.0627

AC:

5376

AN:

85712

European-Finnish (FIN)

AF:

0.0696

AC:

3710

AN:

53274

Middle Eastern (MID)

AF:

0.0744

AC:

428

AN:

5752

European-Non Finnish (NFE)

AF:

0.0564

AC:

62555

AN:

1110036

Other (OTH)

AF:

0.0635

AC:

3827

AN:

60264

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.482

Heterozygous variant carriers

4129

8258

12388

16517

20646

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

2408

4816

7224

9632

12040

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0512

AC:

7793

AN:

152338

Hom.:

286

Cov.:

AF XY:

0.0515

AC XY:

3839

AN XY:

74480

show subpopulations

African (AFR)

AF:

0.0162

AC:

674

AN:

41588

American (AMR)

AF:

0.0616

AC:

942

AN:

15304

Ashkenazi Jewish (ASJ)

AF:

0.130

AC:

451

AN:

3468

East Asian (EAS)

AF:

0.121

AC:

630

AN:

5188

South Asian (SAS)

AF:

0.0578

AC:

279

AN:

4824

European-Finnish (FIN)

AF:

0.0604

AC:

641

AN:

10616

Middle Eastern (MID)

AF:

0.0680

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0572

AC:

3892

AN:

68028

Other (OTH)

AF:

0.0647

AC:

137

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.496

Heterozygous variant carriers

373

746

1120

1493

1866

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

192

288

384

480

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0578

Hom.:

217

Bravo

AF:

0.0511

Asia WGS

AF:

0.0670

AC:

232

AN:

3478

EpiCase

AF:

0.0650

EpiControl

AF:

0.0642

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.46

CADD

Benign

(source)

DANN

Benign

0.89

PhyloP100

1.0

Mutation Taster

=86/14

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over