rs7075893

Variant names:

• chr10-91216856-T-C
• rs7075893
• ENST00000614189.4:c.-183-5833T>C

Variant summary

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

The ENST00000614189.4(PCGF5):​c.-183-5833T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0503 in 152,234 control chromosomes in the GnomAD database, including 624 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 0.050 (624 hom., cov: 32)
• Consequence: PCGF5 ENST00000614189.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.57
• Publications: 0 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=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.168 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PCGF5	NM_001257101.2	c.-183-5833T>C		intron_variant	Intron 1 of 9		NP_001244030.1
PCGF5	NR_046435.1	n.71-5833T>C		intron_variant	Intron 1 of 2
PCGF5	XM_017016776.3	c.-183-5833T>C		intron_variant	Intron 1 of 9		XP_016872265.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PCGF5	ENST00000614189.4	c.-183-5833T>C		intron_variant	Intron 1 of 9	1		ENSP00000479492.1

Frequencies

GnomAD3 genomes AF: 0.0502 AC: 7630 AN: 152116 Hom.: 621 Cov.: 32

Gnomad AFR AF: 0.172

Gnomad AMI AF: 0.0329

Gnomad AMR AF: 0.0209

Gnomad ASJ AF: 0.00518

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00145

Gnomad FIN AF: 0.0000941

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.00126

Gnomad OTH AF: 0.0339

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

GnomAD4 genome AF: 0.0503 AC: 7657 AN: 152234 Hom.: 624 Cov.: 32 AF XY: 0.0484 AC XY: 3600 AN XY: 74430

African (AFR) AF: 0.172 AC: 7122 AN: 41484

American (AMR) AF: 0.0208 AC: 319 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.00518 AC: 18 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5192

South Asian (SAS) AF: 0.00145 AC: 7 AN: 4828

European-Finnish (FIN) AF: 0.0000941 AC: 1 AN: 10624

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.00126 AC: 86 AN: 68008

Other (OTH) AF: 0.0336 AC: 71 AN: 2114

Alfa AF: 0.0386 Hom.: 37

Bravo AF: 0.0574

Asia WGS AF: 0.00953 AC: 33 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	9.9
DANN	Benign	0.56
PhyloP100		1.6

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

Other links and lift over

dbSNP: rs7075893; hg19: chr10-92976613;