rs3785125

Variant names:

• chr16-68354489-T-A
• rs3785125
• NM_019023.5:c.1650+923T>A

Your query was ambiguous. Multiple possible variants found:

• chr16-68354489-T-A
• chr16-68354489-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_019023.5(PRMT7):​c.1650+923T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.555 in 152,200 control chromosomes in the GnomAD database, including 23,815 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 0.55 (23814 hom., cov: 34)
  • Exomes 𝑓: 0.42 (1 hom.)
• Consequence: PRMT7 NM_019023.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00700

Genes affected

PRMT7 (HGNC:25557): (protein arginine methyltransferase 7) This gene encodes a member of the protein arginine N-methyltransferase family of proteins. The encoded enzyme transfers single methyl groups to arginine residues to generate monomethylarginines on histone proteins as well as other protein substrates. This enzyme plays a role in a wide range of biological processes, including neuronal differentiation, male germ line imprinting, small nuclear ribonucleoprotein biogenesis, and regulation of the Wnt signaling pathway. Mutations in this gene underlie multiple related syndromes in human patients characterized by intellectual disability, short stature and other features. The encoded protein may promote breast cancer cell invasion and metastasis in human patients. [provided by RefSeq, May 2017]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.766 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PRMT7	NM_019023.5	c.1650+923T>A		intron_variant	Intron 16 of 18	ENST00000441236.3	NP_061896.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PRMT7	ENST00000441236.3	c.1650+923T>A		intron_variant	Intron 16 of 18	1	NM_019023.5	ENSP00000409324.2

Frequencies

GnomAD3 genomes AF: 0.555 AC: 84349 AN: 152056 Hom.: 23786 Cov.: 34

Gnomad AFR AF: 0.571

Gnomad AMI AF: 0.428

Gnomad AMR AF: 0.611

Gnomad ASJ AF: 0.380

Gnomad EAS AF: 0.785

Gnomad SAS AF: 0.508

Gnomad FIN AF: 0.475

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.542

Gnomad OTH AF: 0.545

GnomAD4 exome AF: 0.423 AC: 11 AN: 26 Hom.: 1 Cov.: 0 AF XY: 0.333 AC XY: 6 AN XY: 18

Gnomad4 AMR exome AF: 0.500

Gnomad4 ASJ exome AF: 0.00

Gnomad4 FIN exome AF: 0.333

Gnomad4 NFE exome AF: 0.500

GnomAD4 genome AF: 0.555 AC: 84422 AN: 152174 Hom.: 23814 Cov.: 34 AF XY: 0.553 AC XY: 41124 AN XY: 74392

Gnomad4 AFR AF: 0.570

Gnomad4 AMR AF: 0.612

Gnomad4 ASJ AF: 0.380

Gnomad4 EAS AF: 0.786

Gnomad4 SAS AF: 0.510

Gnomad4 FIN AF: 0.475

Gnomad4 NFE AF: 0.542

Gnomad4 OTH AF: 0.539

Alfa AF: 0.549 Hom.: 2846

Bravo AF: 0.568

Asia WGS AF: 0.561 AC: 1952 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.8
DANN	Benign	0.50

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: rs3785125; hg19: chr16-68388392;