rs174532
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001127392.3(MYRF):c.2764+73G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.255 in 1,571,074 control chromosomes in the GnomAD database, including 58,104 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.20 ( 4099 hom., cov: 33)
Exomes 𝑓: 0.26 ( 54005 hom. )
Consequence
MYRF
NM_001127392.3 intron
NM_001127392.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.590
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]
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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=-0.82).
BP6
?
Variant 11-61781402-G-A is Benign according to our data. Variant chr11-61781402-G-A is described in ClinVar as [Benign]. Clinvar id is 1257534.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.29 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MYRF | NM_001127392.3 | c.2764+73G>A | intron_variant | ENST00000278836.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MYRF | ENST00000278836.10 | c.2764+73G>A | intron_variant | 1 | NM_001127392.3 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.199 AC: 30325AN: 152108Hom.: 4099 Cov.: 33
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GnomAD4 exome AF: 0.261 AC: 370919AN: 1418848Hom.: 54005 Cov.: 31 AF XY: 0.256 AC XY: 179717AN XY: 702446
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GnomAD4 genome ? AF: 0.199 AC: 30317AN: 152226Hom.: 4099 Cov.: 33 AF XY: 0.194 AC XY: 14419AN XY: 74414
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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
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at