chr21-46661896-G-A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_206962.4(PRMT2):c.1057G>A(p.Gly353Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00399 in 1,487,760 control chromosomes in the GnomAD database, including 27 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0037 ( 2 hom., cov: 26)
Exomes 𝑓: 0.0040 ( 25 hom. )
Consequence
PRMT2
NM_206962.4 missense
NM_206962.4 missense
Scores
2
15
Clinical Significance
Conservation
PhyloP100: 1.85
Genes affected
PRMT2 (HGNC:5186): (protein arginine methyltransferase 2) Enables several functions, including nuclear receptor binding activity; peroxisome proliferator activated receptor binding activity; and protein homodimerization activity. Involved in several processes, including histone methylation; regulation of androgen receptor signaling pathway; and regulation of transcription, DNA-templated. Located in cytosol and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.004463196).
BP6
?
Variant 21-46661896-G-A is Benign according to our data. Variant chr21-46661896-G-A is described in ClinVar as [Benign]. Clinvar id is 718694.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
?
High Homozygotes in GnomAd at 2 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PRMT2 | NM_206962.4 | c.1057G>A | p.Gly353Arg | missense_variant | 10/12 | ENST00000355680.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PRMT2 | ENST00000355680.8 | c.1057G>A | p.Gly353Arg | missense_variant | 10/12 | 1 | NM_206962.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00367 AC: 546AN: 148842Hom.: 2 Cov.: 26
GnomAD3 genomes
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GnomAD3 exomes AF: 0.00401 AC: 676AN: 168482Hom.: 6 AF XY: 0.00390 AC XY: 372AN XY: 95412
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GnomAD4 exome AF: 0.00403 AC: 5394AN: 1338810Hom.: 25 Cov.: 32 AF XY: 0.00392 AC XY: 2601AN XY: 662684
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GnomAD4 genome ? AF: 0.00366 AC: 545AN: 148950Hom.: 2 Cov.: 26 AF XY: 0.00386 AC XY: 280AN XY: 72632
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jun 22, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Uncertain
Dann
Uncertain
DEOGEN2
Benign
T;T;T;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
MetaRNN
Benign
T;T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
L;L;L;.
MutationTaster
Benign
D;D;D;D;D;D;N
PrimateAI
Benign
T
PROVEAN
Benign
N;N;N;N
REVEL
Benign
Sift
Benign
T;T;T;T
Sift4G
Benign
T;T;T;T
Polyphen
B;B;B;.
Vest4
MutPred
Loss of catalytic residue at E352 (P = 0.1736);Loss of catalytic residue at E352 (P = 0.1736);Loss of catalytic residue at E352 (P = 0.1736);.;
MVP
MPC
1.2
ClinPred
T
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at