rs55903902

chr11-61764519-A-G

Variant summary

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

The NM_001127392.3(MYRF):c.47-1106A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.195 in 152,088 control chromosomes in the GnomAD database, including 3,307 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 0.19 (3307 hom., cov: 33)
• Consequence: MYRF NM_001127392.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0170

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.281 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MYRF	NM_001127392.3	c.47-1106A>G		intron_variant		ENST00000278836.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MYRF	ENST00000278836.10	c.47-1106A>G		intron_variant		1	NM_001127392.3	P2
MYRF	ENST00000265460.9	c.20-1106A>G		intron_variant		1		A2
MYRF	ENST00000537766.1	n.150-1106A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.195 AC: 29617 AN: 151970 Hom.: 3309 Cov.: 33

Gnomad AFR AF: 0.0988

Gnomad AMI AF: 0.288

Gnomad AMR AF: 0.289

Gnomad ASJ AF: 0.245

Gnomad EAS AF: 0.284

Gnomad SAS AF: 0.225

Gnomad FIN AF: 0.124

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.229

Gnomad OTH AF: 0.239

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

GnomAD4 genome AF: 0.195 AC: 29616 AN: 152088 Hom.: 3307 Cov.: 33 AF XY: 0.190 AC XY: 14147 AN XY: 74358

Gnomad4 AFR AF: 0.0985

Gnomad4 AMR AF: 0.289

Gnomad4 ASJ AF: 0.245

Gnomad4 EAS AF: 0.285

Gnomad4 SAS AF: 0.225

Gnomad4 FIN AF: 0.124

Gnomad4 NFE AF: 0.229

Gnomad4 OTH AF: 0.239

Alfa AF: 0.208 Hom.: 633

Bravo AF: 0.203

Asia WGS AF: 0.256 AC: 891 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
Cadd	Benign	8.5
Dann	Benign	0.92

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: rs55903902; hg19: chr11-61531991;