chr11-61770306-G-A
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 1P and 12B. PP2BP4_ModerateBP6_ModerateBS1BS2
The NM_001127392.3(MYRF):c.521G>A(p.Arg174His) variant causes a missense change. The variant allele was found at a frequency of 0.000801 in 1,602,592 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R174C) has been classified as Uncertain significance.
Frequency
Consequence
NM_001127392.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MYRF | NM_001127392.3 | c.521G>A | p.Arg174His | missense_variant | 5/27 | ENST00000278836.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MYRF | ENST00000278836.10 | c.521G>A | p.Arg174His | missense_variant | 5/27 | 1 | NM_001127392.3 | P2 | |
MYRF | ENST00000265460.9 | c.494G>A | p.Arg165His | missense_variant | 5/26 | 1 | A2 | ||
MYRF | ENST00000675319.1 | c.106-1194G>A | intron_variant | ||||||
TMEM258 | ENST00000535042.1 | n.649-1533C>T | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.000533 AC: 81AN: 151850Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000642 AC: 146AN: 227280Hom.: 1 AF XY: 0.000675 AC XY: 84AN XY: 124362
GnomAD4 exome AF: 0.000829 AC: 1202AN: 1450742Hom.: 1 Cov.: 33 AF XY: 0.000849 AC XY: 612AN XY: 721176
GnomAD4 genome ? AF: 0.000533 AC: 81AN: 151850Hom.: 0 Cov.: 32 AF XY: 0.000485 AC XY: 36AN XY: 74156
ClinVar
Submissions by phenotype
MYRF-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jul 11, 2022 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at