rs917587

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.67
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

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
PRMT8NM_001256536.1 linkuse as main transcriptc.48+52067G>A intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
PRMT8ENST00000452611.6 linkuse as main transcriptc.48+52067G>A intron_variant 1 Q9NR22-2

Frequencies

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs917587; hg19: chr12-3542675; API