Variant chr11-61755487-G-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_001127392.3(MYRF):c.46+2697G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0105 in 1,600,060 control chromosomes in the GnomAD database, including 815 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.018 ( 93 hom., cov: 33)

Exomes 𝑓: 0.0097 ( 722 hom. )

Consequence

MYRF
NM_001127392.3 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.956

Variant links:

Genes affected

MYRF (HGNC:1181): (myelin regulatory factor) This gene encodes a transcription factor that is required for central nervous system myelination and may regulate oligodendrocyte differentiation. It is thought to act by increasing the expression of genes that effect myelin production but may also directly promote myelin gene expression. Loss of a similar gene in mouse models results in severe demyelination. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Nov 2014]

MYRF links:

MYRF-AS1 (HGNC:24506): (MYRF antisense RNA 1)

MYRF-AS1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BP6

Variant 11-61755487-G-T is Benign according to our data. Variant chr11-61755487-G-T is described in ClinVar as [Benign]. Clinvar id is 1246473.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.116 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MYRF	NM_001127392.3 linkuse as main transcript	c.46+2697G>T		intron_variant		ENST00000278836.10
MYRF-AS1	NR_026882.1 linkuse as main transcript	n.519+148C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MYRF	ENST00000278836.10 linkuse as main transcript	c.46+2697G>T		intron_variant		1	NM_001127392.3	P2	Q9Y2G1-1
MYRF-AS1	ENST00000536405.5 linkuse as main transcript	n.504+148C>A		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes

AF:

0.0179

AC:

2717

AN:

152140

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0368

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00641

Gnomad ASJ

AF:

0.00144

Gnomad EAS

AF:

0.124

Gnomad SAS

AF:

0.0782

Gnomad FIN

AF:

0.0000941

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000544

Gnomad OTH

AF:

0.0163

GnomAD3 exomes

AF:

0.0215

AC:

5130

AN:

238196

Hom.:

223

AF XY:

0.0234

AC XY:

3038

AN XY:

129680

show subpopulations

Gnomad AFR exome

AF:

0.0364

Gnomad AMR exome

AF:

0.00365

Gnomad ASJ exome

AF:

0.000953

Gnomad EAS exome

AF:

0.128

Gnomad SAS exome

AF:

0.0711

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000472

Gnomad OTH exome

AF:

0.00887

GnomAD4 exome

AF:

0.00973

AC:

14092

AN:

1447802

Hom.:

722

Cov.:

AF XY:

0.0113

AC XY:

8166

AN XY:

720630

show subpopulations

Gnomad4 AFR exome

AF:

0.0340

Gnomad4 AMR exome

AF:

0.00375

Gnomad4 ASJ exome

AF:

0.00136

Gnomad4 EAS exome

AF:

0.139

Gnomad4 SAS exome

AF:

0.0693

Gnomad4 FIN exome

AF:

0.0000192

Gnomad4 NFE exome

AF:

0.000265

Gnomad4 OTH exome

AF:

0.0176

GnomAD4 genome

AF:

0.0179

AC:

2719

AN:

152258

Hom.:

Cov.:

AF XY:

0.0191

AC XY:

1419

AN XY:

74448

show subpopulations

Gnomad4 AFR

AF:

0.0367

Gnomad4 AMR

AF:

0.00640

Gnomad4 ASJ

AF:

0.00144

Gnomad4 EAS

AF:

0.124

Gnomad4 SAS

AF:

0.0774

Gnomad4 FIN

AF:

0.0000941

Gnomad4 NFE

AF:

0.000544

Gnomad4 OTH

AF:

0.0175

Alfa

AF:

0.00399

Hom.:

Bravo

AF:

0.0169

Asia WGS

AF:

0.0860

AC:

298

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

GeneDx

May 13, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

5.8

DANN

Benign

0.67

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.3

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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