rs1893495

Positions:

• chr18-13759429-G-A
• chr18-13759429-G-C
• chr18-13759429-G-T

Variant summary

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

The NM_003799.3(RNMT):​c.1394-513G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.603 in 151,882 control chromosomes in the GnomAD database, including 28,322 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 0.60 (28322 hom., cov: 31)
• Consequence: RNMT NM_003799.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.46

Genes affected

RNMT (HGNC:10075): (RNA guanine-7 methyltransferase) Enables RNA binding activity and mRNA (guanine-N7-)-methyltransferase activity. Involved in 7-methylguanosine mRNA capping. Located in fibrillar center and nucleoplasm. Part of mRNA cap binding activity complex; mRNA cap methyltransferase complex; and receptor complex. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.841 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RNMT	NM_003799.3	c.1394-513G>A		intron_variant		ENST00000383314.7	NP_003790.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RNMT	ENST00000383314.7	c.1394-513G>A		intron_variant		1	NM_003799.3	ENSP00000372804	P1

Frequencies

GnomAD3 genomes AF: 0.602 AC: 91405 AN: 151764 Hom.: 28278 Cov.: 31

Gnomad AFR AF: 0.707

Gnomad AMI AF: 0.369

Gnomad AMR AF: 0.652

Gnomad ASJ AF: 0.549

Gnomad EAS AF: 0.862

Gnomad SAS AF: 0.614

Gnomad FIN AF: 0.530

Gnomad MID AF: 0.566

Gnomad NFE AF: 0.525

Gnomad OTH AF: 0.570

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.603 AC: 91509 AN: 151882 Hom.: 28322 Cov.: 31 AF XY: 0.604 AC XY: 44848 AN XY: 74200

Gnomad4 AFR AF: 0.707

Gnomad4 AMR AF: 0.652

Gnomad4 ASJ AF: 0.549

Gnomad4 EAS AF: 0.862

Gnomad4 SAS AF: 0.614

Gnomad4 FIN AF: 0.530

Gnomad4 NFE AF: 0.525

Gnomad4 OTH AF: 0.575

Alfa AF: 0.552 Hom.: 4773

Bravo AF: 0.619

Asia WGS AF: 0.736 AC: 2557 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.017
DANN	Benign	0.56

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: rs1893495; hg19: chr18-13759428;