rs4766119

Positions:

• chr12-3439590-G-A
• chr12-3439590-G-C

Variant summary

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

The NM_001256536.1(PRMT8):​c.48+58148G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.848 in 152,228 control chromosomes in the GnomAD database, including 55,284 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 0.85 (55284 hom., cov: 33)
• Consequence: PRMT8 NM_001256536.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.299

Genes affected

PRMT8 (HGNC:5188): (protein arginine methyltransferase 8) Arginine methylation is a widespread posttranslational modification mediated by arginine methyltransferases, such as PRMT8. Arginine methylation is involved in a number of cellular processes, including DNA repair, RNA transcription, signal transduction, protein compartmentalization, and possibly protein translation (Lee et al., 2005 [PubMed 16051612]).[supplied by OMIM, Mar 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.905 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PRMT8	NM_001256536.1	c.48+58148G>A		intron_variant			NP_001243465.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PRMT8	ENST00000452611.6	c.48+58148G>A		intron_variant		1		ENSP00000414507.2

Frequencies

GnomAD3 genomes AF: 0.848 AC: 129006 AN: 152110 Hom.: 55239 Cov.: 33

Gnomad AFR AF: 0.733

Gnomad AMI AF: 0.946

Gnomad AMR AF: 0.842

Gnomad ASJ AF: 0.925

Gnomad EAS AF: 0.834

Gnomad SAS AF: 0.731

Gnomad FIN AF: 0.928

Gnomad MID AF: 0.820

Gnomad NFE AF: 0.911

Gnomad OTH AF: 0.848

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

GnomAD4 genome AF: 0.848 AC: 129106 AN: 152228 Hom.: 55284 Cov.: 33 AF XY: 0.846 AC XY: 62951 AN XY: 74436

Gnomad4 AFR AF: 0.733

Gnomad4 AMR AF: 0.843

Gnomad4 ASJ AF: 0.925

Gnomad4 EAS AF: 0.833

Gnomad4 SAS AF: 0.732

Gnomad4 FIN AF: 0.928

Gnomad4 NFE AF: 0.911

Gnomad4 OTH AF: 0.849

Alfa AF: 0.893 Hom.: 126526

Bravo AF: 0.837

Asia WGS AF: 0.794 AC: 2761 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.78
DANN	Benign	0.40

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs4766119; hg19: chr12-3548756;