Variant 18-13746277-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2

The NM_003799.3(RNMT):c.1197C>T(p.Tyr399=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00645 in 1,574,236 control chromosomes in the GnomAD database, including 41 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0051 ( 4 hom., cov: 33)

Exomes 𝑓: 0.0066 ( 37 hom. )

Consequence

RNMT
NM_003799.3 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 2.47

Variant links:

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]

RNMT links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.41).

BP6

Variant 18-13746277-C-T is Benign according to our data. Variant chr18-13746277-C-T is described in ClinVar as [Benign]. Clinvar id is 773596.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=2.47 with no splicing effect.

BS2

High Homozygotes in GnomAd4 at 4 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RNMT	NM_003799.3 linkuse as main transcript	c.1197C>T	p.Tyr399=	synonymous_variant	9/12	ENST00000383314.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RNMT	ENST00000383314.7 linkuse as main transcript	c.1197C>T	p.Tyr399=	synonymous_variant	9/12	1	NM_003799.3	P1	O43148-1

Frequencies

GnomAD3 genomes

AF:

0.00514

AC:

781

AN:

152006

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000991

Gnomad AMI

AF:

0.0208

Gnomad AMR

AF:

0.00151

Gnomad ASJ

AF:

0.00231

Gnomad EAS

AF:

0.00193

Gnomad SAS

AF:

0.00145

Gnomad FIN

AF:

0.00578

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00888

Gnomad OTH

AF:

0.00383

GnomAD3 exomes

AF:

0.00522

AC:

1246

AN:

238522

Hom.:

AF XY:

0.00515

AC XY:

668

AN XY:

129604

show subpopulations

Gnomad AFR exome

AF:

0.00127

Gnomad AMR exome

AF:

0.00128

Gnomad ASJ exome

AF:

0.00250

Gnomad EAS exome

AF:

0.00225

Gnomad SAS exome

AF:

0.00195

Gnomad FIN exome

AF:

0.00564

Gnomad NFE exome

AF:

0.00838

Gnomad OTH exome

AF:

0.00414

GnomAD4 exome

AF:

0.00659

AC:

9373

AN:

1422112

Hom.:

Cov.:

AF XY:

0.00647

AC XY:

4593

AN XY:

709484

show subpopulations

Gnomad4 AFR exome

AF:

0.00145

Gnomad4 AMR exome

AF:

0.00151

Gnomad4 ASJ exome

AF:

0.00242

Gnomad4 EAS exome

AF:

0.00194

Gnomad4 SAS exome

AF:

0.00191

Gnomad4 FIN exome

AF:

0.00595

Gnomad4 NFE exome

AF:

0.00768

Gnomad4 OTH exome

AF:

0.00537

GnomAD4 genome

AF:

0.00513

AC:

781

AN:

152124

Hom.:

Cov.:

AF XY:

0.00473

AC XY:

352

AN XY:

74352

show subpopulations

Gnomad4 AFR

AF:

0.000988

Gnomad4 AMR

AF:

0.00150

Gnomad4 ASJ

AF:

0.00231

Gnomad4 EAS

AF:

0.00193

Gnomad4 SAS

AF:

0.00145

Gnomad4 FIN

AF:

0.00578

Gnomad4 NFE

AF:

0.00888

Gnomad4 OTH

AF:

0.00379

Alfa

AF:

0.00796

Hom.:

Bravo

AF:

0.00507

Asia WGS

AF:

0.00144

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Apr 07, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.41

CADD

Benign

DANN

Benign

0.45

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

2.7

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over