11-61766325-A-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_001127392.3(MYRF):c.398+104A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.396 in 1,293,288 control chromosomes in the GnomAD database, including 109,431 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.35 (10447 hom., cov: 32)
  • Exomes 𝑓: 0.40 (98984 hom.)
• Consequence: MYRF NM_001127392.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.690

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]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BP6: Variant 11-61766325-A-T is Benign according to our data. Variant chr11-61766325-A-T is described in ClinVar as [Benign]. Clinvar id is 1268050.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.44 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MYRF	NM_001127392.3	c.398+104A>T		intron_variant		ENST00000278836.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MYRF	ENST00000278836.10	c.398+104A>T		intron_variant		1	NM_001127392.3	P2
MYRF	ENST00000265460.9	c.371+104A>T		intron_variant		1		A2
MYRF	ENST00000675319.1	c.105+104A>T		intron_variant
MYRF	ENST00000537766.1	n.850A>T		non_coding_transcript_exon_variant	2/2	3

Frequencies

GnomAD3 genomes AF: 0.346 AC: 52488 AN: 151780 Hom.: 10443 Cov.: 32

Gnomad AFR AF: 0.204

Gnomad AMI AF: 0.584

Gnomad AMR AF: 0.312

Gnomad ASJ AF: 0.533

Gnomad EAS AF: 0.0141

Gnomad SAS AF: 0.147

Gnomad FIN AF: 0.482

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.444

Gnomad OTH AF: 0.359

GnomAD4 exome AF: 0.403 AC: 460008 AN: 1141390 Hom.: 98984 Cov.: 15 AF XY: 0.398 AC XY: 222297 AN XY: 557946

Gnomad4 AFR exome AF: 0.202

Gnomad4 AMR exome AF: 0.260

Gnomad4 ASJ exome AF: 0.526

Gnomad4 EAS exome AF: 0.0109

Gnomad4 SAS exome AF: 0.174

Gnomad4 FIN exome AF: 0.485

Gnomad4 NFE exome AF: 0.437

Gnomad4 OTH exome AF: 0.381

GnomAD4 genome AF: 0.346 AC: 52490 AN: 151898 Hom.: 10447 Cov.: 32 AF XY: 0.344 AC XY: 25571 AN XY: 74276

Gnomad4 AFR AF: 0.204

Gnomad4 AMR AF: 0.311

Gnomad4 ASJ AF: 0.533

Gnomad4 EAS AF: 0.0141

Gnomad4 SAS AF: 0.148

Gnomad4 FIN AF: 0.482

Gnomad4 NFE AF: 0.444

Gnomad4 OTH AF: 0.355

Alfa AF: 0.245 Hom.: 596

Bravo AF: 0.327

Asia WGS AF: 0.102 AC: 356 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 13, 2021

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	0.75
Dann	Benign	0.67

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: rs4963418; hg19: chr11-61533797;