Variant chr17-36602169-G-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The ENST00000614766.5(MRM1):c.359G>C(p.Cys120Ser) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0525 in 1,612,390 control chromosomes in the GnomAD database, including 2,909 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.050 ( 320 hom., cov: 32)

Exomes 𝑓: 0.053 ( 2589 hom. )

Consequence

MRM1
ENST00000614766.5 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 8.48

Variant links:

Genes affected

MRM1 (HGNC:26202): (mitochondrial rRNA methyltransferase 1) Enables rRNA (guanosine-2'-O-)-methyltransferase activity. Predicted to be involved in rRNA 2'-O-methylation. Located in mitochondrion. [provided by Alliance of Genome Resources, Apr 2022]

MRM1 links:

MRM1 (HGNC:):

MRM1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0023248196).

BP6

Variant 17-36602169-G-C is Benign according to our data. Variant chr17-36602169-G-C is described in ClinVar as [Benign]. Clinvar id is 1685657.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.155 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MRM1	NM_024864.5 linkuse as main transcript	c.359G>C	p.Cys120Ser	missense_variant	1/5	ENST00000614766.5	NP_079140.2	Q6IN84-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MRM1	ENST00000614766.5 linkuse as main transcript	c.359G>C	p.Cys120Ser	missense_variant	1/5	1	NM_024864.5	ENSP00000481559.1		Q6IN84-1
MRM1	ENST00000612760.1 linkuse as main transcript	c.-51G>C		5_prime_UTR_variant	1/5	1		ENSP00000482526.1		A0A087WZC1

Frequencies

GnomAD3 genomes

AF:

0.0497

AC:

7561

AN:

152146

Hom.:

314

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00919

Gnomad AMI

AF:

0.145

Gnomad AMR

AF:

0.0612

Gnomad ASJ

AF:

0.0631

Gnomad EAS

AF:

0.164

Gnomad SAS

AF:

0.0792

Gnomad FIN

AF:

0.133

Gnomad MID

AF:

0.0475

Gnomad NFE

AF:

0.0459

Gnomad OTH

AF:

0.0560

GnomAD3 exomes

AF:

0.0642

AC:

15668

AN:

244080

Hom.:

689

AF XY:

0.0648

AC XY:

8644

AN XY:

133400

show subpopulations

Gnomad AFR exome

AF:

0.00753

Gnomad AMR exome

AF:

0.0433

Gnomad ASJ exome

AF:

0.0629

Gnomad EAS exome

AF:

0.180

Gnomad SAS exome

AF:

0.0647

Gnomad FIN exome

AF:

0.127

Gnomad NFE exome

AF:

0.0471

Gnomad OTH exome

AF:

0.0616

GnomAD4 exome

AF:

0.0528

AC:

77047

AN:

1460126

Hom.:

2589

Cov.:

AF XY:

0.0533

AC XY:

38722

AN XY:

726142

show subpopulations

Gnomad4 AFR exome

AF:

0.00876

Gnomad4 AMR exome

AF:

0.0443

Gnomad4 ASJ exome

AF:

0.0631

Gnomad4 EAS exome

AF:

0.175

Gnomad4 SAS exome

AF:

0.0665

Gnomad4 FIN exome

AF:

0.126

Gnomad4 NFE exome

AF:

0.0449

Gnomad4 OTH exome

AF:

0.0589

GnomAD4 genome

AF:

0.0497

AC:

7569

AN:

152264

Hom.:

320

Cov.:

AF XY:

0.0557

AC XY:

4143

AN XY:

74444

show subpopulations

Gnomad4 AFR

AF:

0.00916

Gnomad4 AMR

AF:

0.0617

Gnomad4 ASJ

AF:

0.0631

Gnomad4 EAS

AF:

0.164

Gnomad4 SAS

AF:

0.0788

Gnomad4 FIN

AF:

0.133

Gnomad4 NFE

AF:

0.0459

Gnomad4 OTH

AF:

0.0578

Alfa

AF:

0.0515

Hom.:

207

Bravo

AF:

0.0422

TwinsUK

AF:

0.0410

AC:

152

ALSPAC

AF:

0.0446

AC:

172

ESP6500AA

AF:

0.00845

AC:

ESP6500EA

AF:

0.0454

AC:

388

ExAC

AF:

0.0597

AC:

7225

Asia WGS

AF:

0.105

AC:

367

AN:

3478

EpiCase

AF:

0.0516

EpiControl

AF:

0.0503

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Mendelics

May 04, 2022

- -

not provided

Benign:1

Benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Pathogenic

0.71

BayesDel_addAF

Benign

-0.27

BayesDel_noAF

Uncertain

-0.020

CADD

Uncertain

DANN

Uncertain

1.0

DEOGEN2

Benign

0.082

Eigen

Pathogenic

0.77

Eigen_PC

Pathogenic

0.74

FATHMM_MKL

Pathogenic

0.98

MetaRNN

Benign

0.0023

MetaSVM

Benign

-1.2

MutationAssessor

Uncertain

2.4

MutationTaster

Benign

1.0

D;D

PrimateAI

Pathogenic

0.81

Sift4G

Uncertain

0.0090

Polyphen

0.97

Vest4

0.30

MutPred

0.74

Gain of disorder (P = 0.0228);

ClinPred

0.029

GERP RS

4.9

Varity_R

0.75

gMVP

0.80

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