rs10415880

Variant names:

• chr19-49685899-G-A
• rs10415880
• NM_001536.6:c.760-194G>A

Your query was ambiguous. Multiple possible variants found:

• chr19-49685899-G-A
• chr19-49685899-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001536.6(PRMT1):​c.760-194G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.308 in 1,408,698 control chromosomes in the GnomAD database, including 70,104 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 0.29 (6812 hom., cov: 31)
  • Exomes 𝑓: 0.31 (63292 hom.)
• Consequence: PRMT1 NM_001536.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.975
• Publications: 28 publications found

Genes affected

PRMT1 (HGNC:5187): (protein arginine methyltransferase 1) This gene encodes a member of the protein arginine N-methyltransferase (PRMT) family. Post-translational modification of target proteins by PRMTs plays an important regulatory role in many biological processes, whereby PRMTs methylate arginine residues by transferring methyl groups from S-adenosyl-L-methionine to terminal guanidino nitrogen atoms. The encoded protein is a type I PRMT and is responsible for the majority of cellular arginine methylation activity. Increased expression of this gene may play a role in many types of cancer. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene, and a pseudogene of this gene is located on the long arm of chromosome 5. [provided by RefSeq, Dec 2011]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.319 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001536.6. 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
	PRMT1	NM_001536.6	MANE Select	c.760-194G>A		intron	N/A	NP_001527.3
	PRMT1	NM_198318.5		c.706-194G>A		intron	N/A	NP_938074.2
	PRMT1	NM_001207042.3		c.502-194G>A		intron	N/A	NP_001193971.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PRMT1	ENST00000454376.7	TSL:1 MANE Select	c.760-194G>A		intron	N/A	ENSP00000406162.2
	PRMT1	ENST00000391851.8	TSL:1	c.706-194G>A		intron	N/A	ENSP00000375724.4
	PRMT1	ENST00000911948.1		c.760-194G>A		intron	N/A	ENSP00000582007.1

Frequencies

GnomAD3 genomes AF: 0.294 AC: 44554 AN: 151786 Hom.: 6803 Cov.: 31

Gnomad AFR AF: 0.318

Gnomad AMI AF: 0.311

Gnomad AMR AF: 0.220

Gnomad ASJ AF: 0.273

Gnomad EAS AF: 0.0216

Gnomad SAS AF: 0.157

Gnomad FIN AF: 0.319

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.322

Gnomad OTH AF: 0.284

GnomAD4 exome AF: 0.309 AC: 388800 AN: 1256794 Hom.: 63292 Cov.: 34 AF XY: 0.306 AC XY: 185844 AN XY: 607908

African (AFR) AF: 0.327 AC: 9043 AN: 27626

American (AMR) AF: 0.188 AC: 3219 AN: 17168

Ashkenazi Jewish (ASJ) AF: 0.273 AC: 4963 AN: 18178

East Asian (EAS) AF: 0.0175 AC: 577 AN: 33060

South Asian (SAS) AF: 0.168 AC: 10063 AN: 59828

European-Finnish (FIN) AF: 0.296 AC: 8524 AN: 28766

Middle Eastern (MID) AF: 0.330 AC: 1152 AN: 3494

European-Non Finnish (NFE) AF: 0.330 AC: 335333 AN: 1016770

Other (OTH) AF: 0.307 AC: 15926 AN: 51904

GnomAD4 genome AF: 0.294 AC: 44588 AN: 151904 Hom.: 6812 Cov.: 31 AF XY: 0.286 AC XY: 21219 AN XY: 74234

African (AFR) AF: 0.318 AC: 13177 AN: 41402

American (AMR) AF: 0.219 AC: 3352 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.273 AC: 946 AN: 3466

East Asian (EAS) AF: 0.0217 AC: 112 AN: 5172

South Asian (SAS) AF: 0.157 AC: 756 AN: 4820

European-Finnish (FIN) AF: 0.319 AC: 3367 AN: 10544

Middle Eastern (MID) AF: 0.327 AC: 96 AN: 294

European-Non Finnish (NFE) AF: 0.322 AC: 21899 AN: 67912

Other (OTH) AF: 0.284 AC: 599 AN: 2108

Alfa AF: 0.311 Hom.: 11988

Bravo AF: 0.289

Asia WGS AF: 0.122 AC: 424 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.75
DANN	Benign	0.63
PhyloP100		-0.97
Mutation Taster		=100/0	polymorphism (auto)

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: rs10415880; hg19: chr19-50189156;