rs2242234

Positions:

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_ModerateBP7BA1

The NM_006315.7(PCGF3):​c.525C>T​(p.Arg175=) 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

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.01
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-AS1 (HGNC:56108): (PCGF3 antisense RNA 1)

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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/exons MANE UniProt
PCGF3NM_006315.7 linkuse as main transcriptc.525C>T p.Arg175= synonymous_variant 9/11 ENST00000362003.10
LOC124900163XM_047416474.1 linkuse as main transcriptc.-1294G>A 5_prime_UTR_variant 2/2
PCGF3-AS1NR_171661.1 linkuse as main transcriptn.3483G>A non_coding_transcript_exon_variant 3/3

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
PCGF3ENST00000362003.10 linkuse as main transcriptc.525C>T p.Arg175= synonymous_variant 9/115 NM_006315.7 P1Q3KNV8-1
PCGF3-AS1ENST00000660016.1 linkuse as main transcriptn.1478G>A non_coding_transcript_exon_variant 2/2

Frequencies

GnomAD3 genomes
AF:
0.0511
AC:
7786
AN:
152220
Hom.:
286
Cov.:
33
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
GnomAD3 exomes
AF:
0.0643
AC:
15911
AN:
247314
Hom.:
681
AF XY:
0.0649
AC XY:
8717
AN XY:
134228
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 SAS exome
AF:
0.0624
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.:
31
AF XY:
0.0609
AC XY:
44157
AN XY:
725046
show subpopulations
Gnomad4 AFR exome
AF:
0.0143
Gnomad4 AMR exome
AF:
0.0636
Gnomad4 ASJ exome
AF:
0.134
Gnomad4 EAS exome
AF:
0.148
Gnomad4 SAS exome
AF:
0.0627
Gnomad4 FIN exome
AF:
0.0696
Gnomad4 NFE exome
AF:
0.0564
Gnomad4 OTH exome
AF:
0.0635
GnomAD4 genome
AF:
0.0512
AC:
7793
AN:
152338
Hom.:
286
Cov.:
33
AF XY:
0.0515
AC XY:
3839
AN XY:
74480
show subpopulations
Gnomad4 AFR
AF:
0.0162
Gnomad4 AMR
AF:
0.0616
Gnomad4 ASJ
AF:
0.130
Gnomad4 EAS
AF:
0.121
Gnomad4 SAS
AF:
0.0578
Gnomad4 FIN
AF:
0.0604
Gnomad4 NFE
AF:
0.0572
Gnomad4 OTH
AF:
0.0647
Alfa
AF:
0.0579
Hom.:
172
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
16
DANN
Benign
0.89

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs2242234; hg19: chr4-755129; COSMIC: COSV62858333; COSMIC: COSV62858333; API