rs11543052

chr21-46636464-T-C

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_Strong BS2

The NM_206962.4(PRMT2):c.-140T>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0107 in 154,982 control chromosomes in the GnomAD database, including 11 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 0.011 (10 hom., cov: 33)
  • Exomes 𝑓: 0.011 (1 hom.)
• Consequence: PRMT2 NM_206962.4 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.319

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

Verdict is Benign. Variant got -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BS2: High Homozygotes in GnomAd at 10 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PRMT2	NM_206962.4	c.-140T>C		5_prime_UTR_variant	2/12	ENST00000355680.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PRMT2	ENST00000355680.8	c.-140T>C		5_prime_UTR_variant	2/12	1	NM_206962.4	P1

Frequencies

GnomAD3 genomes AF: 0.0107 AC: 1622 AN: 152216 Hom.: 10 Cov.: 33

Gnomad AFR AF: 0.00265

Gnomad AMI AF: 0.0351

Gnomad AMR AF: 0.00811

Gnomad ASJ AF: 0.00115

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00310

Gnomad FIN AF: 0.0320

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0143

Gnomad OTH AF: 0.0110

GnomAD4 exome AF: 0.0113 AC: 30 AN: 2648 Hom.: 1 Cov.: 0 AF XY: 0.0109 AC XY: 15 AN XY: 1376

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00309

Gnomad4 FIN exome AF: 0.0319

Gnomad4 NFE exome AF: 0.0139

Gnomad4 OTH exome AF: 0.00704

GnomAD4 genome AF: 0.0106 AC: 1621 AN: 152334 Hom.: 10 Cov.: 33 AF XY: 0.0112 AC XY: 831 AN XY: 74484

Gnomad4 AFR AF: 0.00265

Gnomad4 AMR AF: 0.00804

Gnomad4 ASJ AF: 0.00115

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00310

Gnomad4 FIN AF: 0.0320

Gnomad4 NFE AF: 0.0143

Gnomad4 OTH AF: 0.0109

Alfa AF: 0.0120 Hom.: 3

Bravo AF: 0.00834

Asia WGS AF: 0.00202 AC: 8 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	4.5
Dann	Benign	0.69
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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

Publications

LitVar

Other links and lift over

dbSNP: rs11543052; hg19: chr21-48056376;