10-91258288-A-C

Variant names:

• chr10-91258288-A-C
• rs2254391
• NM_032373.5:c.475-3038A>C

Variant summary

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

The NM_032373.5(PCGF5):​c.475-3038A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.49 in 151,976 control chromosomes in the GnomAD database, including 21,096 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 0.49 (21096 hom., cov: 32)
• Consequence: PCGF5 NM_032373.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.310
• Publications: 2 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=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.783 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_032373.5. 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_032373.5	MANE Select	c.475-3038A>C		intron	N/A	NP_115749.2
	PCGF5	NM_001256549.2		c.475-3038A>C		intron	N/A	NP_001243478.1	Q86SE9-1
	PCGF5	NM_001257101.2		c.475-3038A>C		intron	N/A	NP_001244030.1	Q86SE9-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PCGF5	ENST00000336126.6	TSL:1 MANE Select	c.475-3038A>C		intron	N/A	ENSP00000337500.5	Q86SE9-1
	PCGF5	ENST00000614189.4	TSL:1	c.475-3038A>C		intron	N/A	ENSP00000479492.1	Q86SE9-1
	PCGF5	ENST00000543648.5	TSL:2	c.475-3038A>C		intron	N/A	ENSP00000445704.1	Q86SE9-1

Frequencies

GnomAD3 genomes AF: 0.490 AC: 74381 AN: 151858 Hom.: 21045 Cov.: 32

Gnomad AFR AF: 0.790

Gnomad AMI AF: 0.256

Gnomad AMR AF: 0.433

Gnomad ASJ AF: 0.353

Gnomad EAS AF: 0.437

Gnomad SAS AF: 0.369

Gnomad FIN AF: 0.297

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.373

Gnomad OTH AF: 0.478

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

GnomAD4 genome AF: 0.490 AC: 74496 AN: 151976 Hom.: 21096 Cov.: 32 AF XY: 0.485 AC XY: 36008 AN XY: 74272

African (AFR) AF: 0.790 AC: 32757 AN: 41454

American (AMR) AF: 0.433 AC: 6601 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.353 AC: 1226 AN: 3470

East Asian (EAS) AF: 0.437 AC: 2257 AN: 5164

South Asian (SAS) AF: 0.368 AC: 1778 AN: 4828

European-Finnish (FIN) AF: 0.297 AC: 3139 AN: 10562

Middle Eastern (MID) AF: 0.459 AC: 135 AN: 294

European-Non Finnish (NFE) AF: 0.373 AC: 25367 AN: 67946

Other (OTH) AF: 0.476 AC: 1003 AN: 2108

Alfa AF: 0.344 Hom.: 1379

Bravo AF: 0.513

Asia WGS AF: 0.411 AC: 1430 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.68
PhyloP100		-0.31
Mutation Taster		=100/0	polymorphism (auto)

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: rs2254391; hg19: chr10-93018045;