Genetic Variant PCGF5:c.112+4770C>T (chr10-91227753-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_032373.5(PCGF5):c.112+4770C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0637 in 999,840 control chromosomes in the GnomAD database, including 3,302 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 0.11 ( 1559 hom., cov: 32)

Exomes 𝑓: 0.056 ( 1743 hom. )

Consequence

PCGF5
NM_032373.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.392

Publications

3 publications found

Variant links:

Genes affected

PCGF5 (HGNC:28264): (polycomb group ring finger 5) Predicted to enable metal ion binding activity. Acts upstream of or within positive regulation of transcription by RNA polymerase II. Located in Golgi apparatus; centrosome; and nucleoplasm. Part of PcG protein complex. [provided by Alliance of Genome Resources, Apr 2022]

PCGF5 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.243 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PCGF5	NM_032373.5 link	c.112+4770C>T		intron_variant	Intron 2 of 9	ENST00000336126.6	NP_115749.2	Q86SE9-1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
PCGF5	ENST00000336126.6 link	c.112+4770C>T	intron_variant	Intron 2 of 9	1	NM_032373.5	ENSP00000337500.5	Q86SE9-1
PCGF5	ENST00000614189.4 link	c.112+4770C>T	intron_variant	Intron 2 of 9	1		ENSP00000479492.1	Q86SE9-1
PCGF5	ENST00000490164.1 link	n.766C>T	non_coding_transcript_exon_variant	Exon 3 of 3	2
PCGF5	ENST00000543648.5 link	c.112+4770C>T	intron_variant	Intron 2 of 9	2		ENSP00000445704.1	Q86SE9-1

Frequencies

GnomAD3 genomes

AF:

0.109

AC:

16558

AN:

151858

Hom.:

1555

Cov.:

show subpopulations

Gnomad AFR

AF:

0.248

Gnomad AMI

AF:

0.0428

Gnomad AMR

AF:

0.0571

Gnomad ASJ

AF:

0.0907

Gnomad EAS

AF:

0.00385

Gnomad SAS

AF:

0.0702

Gnomad FIN

AF:

0.0690

Gnomad MID

AF:

0.101

Gnomad NFE

AF:

0.0558

Gnomad OTH

AF:

0.0962

GnomAD4 exome

AF:

0.0556

AC:

47144

AN:

847864

Hom.:

1743

Cov.:

AF XY:

0.0551

AC XY:

21637

AN XY:

392708

show subpopulations

African (AFR)

AF:

0.257

AC:

4098

AN:

15968

American (AMR)

AF:

0.0370

AC:

AN:

2516

Ashkenazi Jewish (ASJ)

AF:

0.0790

AC:

437

AN:

5532

East Asian (EAS)

AF:

0.00166

AC:

AN:

4212

South Asian (SAS)

AF:

0.0762

AC:

1412

AN:

18540

European-Finnish (FIN)

AF:

0.0439

AC:

AN:

866

Middle Eastern (MID)

AF:

0.109

AC:

184

AN:

1686

European-Non Finnish (NFE)

AF:

0.0506

AC:

38972

AN:

770490

Other (OTH)

AF:

0.0678

AC:

1903

AN:

28054

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.486

Heterozygous variant carriers

2403

4806

7210

9613

12016

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

2072

4144

6216

8288

10360

<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:

0.109

AC:

16573

AN:

151976

Hom.:

1559

Cov.:

AF XY:

0.108

AC XY:

8024

AN XY:

74328

show subpopulations

African (AFR)

AF:

0.247

AC:

10231

AN:

41370

American (AMR)

AF:

0.0570

AC:

870

AN:

15268

Ashkenazi Jewish (ASJ)

AF:

0.0907

AC:

315

AN:

3472

East Asian (EAS)

AF:

0.00386

AC:

AN:

5184

South Asian (SAS)

AF:

0.0707

AC:

340

AN:

4810

European-Finnish (FIN)

AF:

0.0690

AC:

731

AN:

10600

Middle Eastern (MID)

AF:

0.109

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0558

AC:

3794

AN:

67954

Other (OTH)

AF:

0.0952

AC:

201

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

668

1336

2005

2673

3341

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

168

336

504

672

840

<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:

0.0710

Hom.:

770

Bravo

AF:

0.112

Asia WGS

AF:

0.0510

AC:

178

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

2.8

(source)

DANN

Benign

0.49

PhyloP100

-0.39

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Mutation Taster

=100/0

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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