rs1057971

Variant summary

Our verdict is Benign. Variant got -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

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.392
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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/exons MANE UniProt
PCGF5NM_032373.5 linkuse as main transcriptc.112+4770C>T intron_variant ENST00000336126.6

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
PCGF5ENST00000336126.6 linkuse as main transcriptc.112+4770C>T intron_variant 1 NM_032373.5 P1Q86SE9-1
PCGF5ENST00000614189.4 linkuse as main transcriptc.112+4770C>T intron_variant 1 P1Q86SE9-1
PCGF5ENST00000543648.5 linkuse as main transcriptc.112+4770C>T intron_variant 2 P1Q86SE9-1
PCGF5ENST00000490164.1 linkuse as main transcriptn.766C>T non_coding_transcript_exon_variant 3/32

Frequencies

GnomAD3 genomes
AF:
0.109
AC:
16558
AN:
151858
Hom.:
1555
Cov.:
32
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.:
29
AF XY:
0.0551
AC XY:
21637
AN XY:
392708
show subpopulations
Gnomad4 AFR exome
AF:
0.257
Gnomad4 AMR exome
AF:
0.0370
Gnomad4 ASJ exome
AF:
0.0790
Gnomad4 EAS exome
AF:
0.00166
Gnomad4 SAS exome
AF:
0.0762
Gnomad4 FIN exome
AF:
0.0439
Gnomad4 NFE exome
AF:
0.0506
Gnomad4 OTH exome
AF:
0.0678
GnomAD4 genome
AF:
0.109
AC:
16573
AN:
151976
Hom.:
1559
Cov.:
32
AF XY:
0.108
AC XY:
8024
AN XY:
74328
show subpopulations
Gnomad4 AFR
AF:
0.247
Gnomad4 AMR
AF:
0.0570
Gnomad4 ASJ
AF:
0.0907
Gnomad4 EAS
AF:
0.00386
Gnomad4 SAS
AF:
0.0707
Gnomad4 FIN
AF:
0.0690
Gnomad4 NFE
AF:
0.0558
Gnomad4 OTH
AF:
0.0952
Alfa
AF:
0.0633
Hom.:
429
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
DANN
Benign
0.49
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1

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: rs1057971; hg19: chr10-92987510; API