chr12-3433509-G-A

Position:

• chr12-3433509-G-A

Variant summary

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

The ENST00000452611.6(PRMT8):​c.48+52067G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.65 in 152,192 control chromosomes in the GnomAD database, including 36,955 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 0.65 (36955 hom., cov: 33)
• Consequence: PRMT8 ENST00000452611.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.67

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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.896 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PRMT8	NM_001256536.1	c.48+52067G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PRMT8	ENST00000452611.6	c.48+52067G>A		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.650 AC: 98861 AN: 152074 Hom.: 36937 Cov.: 33

Gnomad AFR AF: 0.254

Gnomad AMI AF: 0.843

Gnomad AMR AF: 0.772

Gnomad ASJ AF: 0.668

Gnomad EAS AF: 0.918

Gnomad SAS AF: 0.727

Gnomad FIN AF: 0.838

Gnomad MID AF: 0.684

Gnomad NFE AF: 0.804

Gnomad OTH AF: 0.675

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

GnomAD4 genome AF: 0.650 AC: 98894 AN: 152192 Hom.: 36955 Cov.: 33 AF XY: 0.655 AC XY: 48722 AN XY: 74424

Gnomad4 AFR AF: 0.253

Gnomad4 AMR AF: 0.773

Gnomad4 ASJ AF: 0.668

Gnomad4 EAS AF: 0.918

Gnomad4 SAS AF: 0.728

Gnomad4 FIN AF: 0.838

Gnomad4 NFE AF: 0.804

Gnomad4 OTH AF: 0.677

Alfa AF: 0.725 Hom.: 6816

Bravo AF: 0.626

Asia WGS AF: 0.764 AC: 2658 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	6.8
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs917587; hg19: chr12-3542675;