rs6583759

chr10-91216813-A-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000614189.4(PCGF5):c.-183-5876A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.162 in 152,162 control chromosomes in the GnomAD database, including 3,944 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 0.16 (3944 hom., cov: 32)
• Consequence: PCGF5 ENST00000614189.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00100

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.408 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PCGF5	NM_001257101.2	c.-183-5876A>C		intron_variant
PCGF5	XM_017016776.3	c.-183-5876A>C		intron_variant
PCGF5	XM_017016777.3	c.-183-5876A>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PCGF5	ENST00000614189.4	c.-183-5876A>C		intron_variant		1		P1

Frequencies

GnomAD3 genomes AF: 0.161 AC: 24544 AN: 152044 Hom.: 3919 Cov.: 32

Gnomad AFR AF: 0.413

Gnomad AMI AF: 0.0428

Gnomad AMR AF: 0.0768

Gnomad ASJ AF: 0.123

Gnomad EAS AF: 0.00346

Gnomad SAS AF: 0.0869

Gnomad FIN AF: 0.0975

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.0597

Gnomad OTH AF: 0.138

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

GnomAD4 genome AF: 0.162 AC: 24615 AN: 152162 Hom.: 3944 Cov.: 32 AF XY: 0.161 AC XY: 11976 AN XY: 74416

Gnomad4 AFR AF: 0.413

Gnomad4 AMR AF: 0.0766

Gnomad4 ASJ AF: 0.123

Gnomad4 EAS AF: 0.00347

Gnomad4 SAS AF: 0.0871

Gnomad4 FIN AF: 0.0975

Gnomad4 NFE AF: 0.0597

Gnomad4 OTH AF: 0.136

Alfa AF: 0.0782 Hom.: 1209

Bravo AF: 0.169

Asia WGS AF: 0.0800 AC: 278 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	6.4
Dann	Benign	0.49

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

Other links and lift over

dbSNP: rs6583759; hg19: chr10-92976570;