3-50353430-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_ModerateBP6_Moderate
The NM_001291284.2(CYB561D2):c.355C>T(p.Arg119Trp) variant causes a missense change. The variant allele was found at a frequency of 0.0000546 in 1,612,978 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict 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. R119L) has been classified as Uncertain significance.
Frequency
Consequence
NM_001291284.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CYB561D2 | NM_001291284.2 | c.355C>T | p.Arg119Trp | missense_variant | 4/4 | ENST00000425346.6 | |
LOC127898564 | NR_183066.1 | n.275+1870C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CYB561D2 | ENST00000425346.6 | c.355C>T | p.Arg119Trp | missense_variant | 4/4 | 1 | NM_001291284.2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000591 AC: 9AN: 152190Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000240 AC: 6AN: 250122Hom.: 0 AF XY: 0.0000222 AC XY: 3AN XY: 135346
GnomAD4 exome AF: 0.0000541 AC: 79AN: 1460670Hom.: 0 Cov.: 31 AF XY: 0.0000550 AC XY: 40AN XY: 726618
GnomAD4 genome AF: 0.0000591 AC: 9AN: 152308Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74472
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 14, 2023 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at