rs2254391

Positions:

• chr10-91258288-A-C
• chr10-91258288-A-G
• chr10-91258288-A-T

Variant summary

Our verdict is Benign. Variant got -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

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=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.783 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PCGF5	NM_032373.5	c.475-3038A>C		intron_variant		ENST00000336126.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PCGF5	ENST00000336126.6	c.475-3038A>C		intron_variant		1	NM_032373.5	P1
PCGF5	ENST00000614189.4	c.475-3038A>C		intron_variant		1		P1
PCGF5	ENST00000543648.5	c.475-3038A>C		intron_variant		2		P1

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

Gnomad4 AFR AF: 0.790

Gnomad4 AMR AF: 0.433

Gnomad4 ASJ AF: 0.353

Gnomad4 EAS AF: 0.437

Gnomad4 SAS AF: 0.368

Gnomad4 FIN AF: 0.297

Gnomad4 NFE AF: 0.373

Gnomad4 OTH AF: 0.476

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.68

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: rs2254391; hg19: chr10-93018045;