rs2839377

Variant names:

• chr21-46657900-C-G
• rs2839377
• NM_206962.4:c.655-845C>G

Your query was ambiguous. Multiple possible variants found:

• chr21-46657900-C-G
• chr21-46657900-C-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_206962.4(PRMT2):​c.655-845C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 34)
• Consequence: PRMT2 NM_206962.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.464
• Publications: 19 publications found

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]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_206962.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PRMT2	NM_206962.4	MANE Select	c.655-845C>G		intron	N/A	NP_996845.1	A0A0S2Z3N3
	PRMT2	NM_001535.5		c.655-845C>G		intron	N/A	NP_001526.2
	PRMT2	NM_001242864.3		c.655-3900C>G		intron	N/A	NP_001229793.1	P55345-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PRMT2	ENST00000355680.8	TSL:1 MANE Select	c.655-845C>G		intron	N/A	ENSP00000347906.3	P55345-1
	PRMT2	ENST00000397638.7	TSL:1	c.655-845C>G		intron	N/A	ENSP00000380760.2	P55345-1
	PRMT2	ENST00000440086.5	TSL:1	c.655-3900C>G		intron	N/A	ENSP00000397266.1	P55345-3

Frequencies

GnomAD3 genomes Cov.: 34

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 34

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.8
DANN	Benign	0.50
PhyloP100		0.46
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs2839377; hg19: chr21-48077812;