chr21-46661935-C-A
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Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_206962.4(PRMT2):c.1096C>A(p.Pro366Thr) variant causes a missense, splice region change. The variant allele was found at a frequency of 0.000152 in 1,294,688 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00021 ( 0 hom., cov: 25)
Exomes 𝑓: 0.00015 ( 0 hom. )
Consequence
PRMT2
NM_206962.4 missense, splice_region
NM_206962.4 missense, splice_region
Scores
8
10
Splicing: ADA: 0.9455
2
Clinical Significance
Conservation
PhyloP100: 4.16
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 Likely_benign. Variant got -4 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.01884982).
BP6
Variant 21-46661935-C-A is Benign according to our data. Variant chr21-46661935-C-A is described in ClinVar as [Likely_benign]. Clinvar id is 764005.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PRMT2 | NM_206962.4 | c.1096C>A | p.Pro366Thr | missense_variant, splice_region_variant | 10/12 | ENST00000355680.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PRMT2 | ENST00000355680.8 | c.1096C>A | p.Pro366Thr | missense_variant, splice_region_variant | 10/12 | 1 | NM_206962.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000205 AC: 29AN: 141274Hom.: 0 Cov.: 25
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GnomAD3 exomes AF: 0.000172 AC: 17AN: 98922Hom.: 0 AF XY: 0.000176 AC XY: 10AN XY: 56882
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GnomAD4 exome AF: 0.000146 AC: 168AN: 1153316Hom.: 0 Cov.: 32 AF XY: 0.000155 AC XY: 87AN XY: 561484
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GnomAD4 genome AF: 0.000205 AC: 29AN: 141372Hom.: 0 Cov.: 25 AF XY: 0.000161 AC XY: 11AN XY: 68340
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jul 18, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Uncertain
D;D;D;.
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
M_CAP
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
Uncertain
T
PROVEAN
Uncertain
D;D;D;D
REVEL
Benign
Sift
Benign
T;T;T;T
Sift4G
Benign
T;T;T;T
Polyphen
D;D;D;.
Vest4
MVP
MPC
1.6
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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Calibrated prediction
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dbscSNV1_ADA
Benign
dbscSNV1_RF
Benign
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at