rs6583759

Variant names:

• chr10-91216813-A-C
• rs6583759
• ENST00000614189.4:c.-183-5876A>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001257101.2(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 NM_001257101.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00100
• Publications: 4 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001257101.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PCGF5	NM_001257101.2		c.-183-5876A>C		intron	N/A	NP_001244030.1	Q86SE9-1
	PCGF5	NR_046435.1		n.71-5876A>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PCGF5	ENST00000614189.4	TSL:1	c.-183-5876A>C		intron	N/A	ENSP00000479492.1	Q86SE9-1
	PCGF5	ENST00000888207.1		c.-183-5876A>C		intron	N/A	ENSP00000558266.1
	PCGF5	ENST00000888212.1		c.-183-5876A>C		intron	N/A	ENSP00000558271.1

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

African (AFR) AF: 0.413 AC: 17116 AN: 41428

American (AMR) AF: 0.0766 AC: 1172 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.123 AC: 428 AN: 3472

East Asian (EAS) AF: 0.00347 AC: 18 AN: 5194

South Asian (SAS) AF: 0.0871 AC: 421 AN: 4832

European-Finnish (FIN) AF: 0.0975 AC: 1034 AN: 10600

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.0597 AC: 4060 AN: 68020

Other (OTH) AF: 0.136 AC: 288 AN: 2112

Alfa AF: 0.0898 Hom.: 2354

Bravo AF: 0.169

Asia WGS AF: 0.0800 AC: 278 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	6.4
DANN	Benign	0.49
PhyloP100		0.0010

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6583759;

hg19: chr10-92976570;