chr17-63440208-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_001915.4(CYB561):c.-13-2648G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0217 in 398,780 control chromosomes in the GnomAD database, including 127 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.019 ( 56 hom., cov: 32)
Exomes 𝑓: 0.023 ( 71 hom. )
Consequence
CYB561
NM_001915.4 intron
NM_001915.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.376
Genes affected
CYB561 (HGNC:2571): (cytochrome b561) Predicted to enable transmembrane monodehydroascorbate reductase activity. Predicted to be involved in ascorbate homeostasis. Predicted to be located in chromaffin granule membrane. Predicted to be active in lysosomal membrane. [provided by Alliance of Genome Resources, Apr 2022]
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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=-0.87).
BP6
?
Variant 17-63440208-C-T is Benign according to our data. Variant chr17-63440208-C-T is described in ClinVar as [Benign]. Clinvar id is 3056754.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0192 (2917/152254) while in subpopulation NFE AF= 0.0304 (2068/68010). AF 95% confidence interval is 0.0293. There are 56 homozygotes in gnomad4. There are 1352 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 56 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CYB561 | NM_001915.4 | c.-13-2648G>A | intron_variant | ENST00000360793.8 | |||
CYB561 | NM_001330421.2 | c.-9G>A | 5_prime_UTR_variant | 1/6 | |||
CYB561 | NM_001017916.2 | c.-13-2648G>A | intron_variant | ||||
CYB561 | NM_001017917.2 | c.-14+519G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CYB561 | ENST00000360793.8 | c.-13-2648G>A | intron_variant | 1 | NM_001915.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0192 AC: 2919AN: 152136Hom.: 56 Cov.: 32
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GnomAD3 exomes AF: 0.0223 AC: 7AN: 314Hom.: 0 AF XY: 0.0128 AC XY: 1AN XY: 78
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GnomAD4 exome AF: 0.0233 AC: 5751AN: 246526Hom.: 71 Cov.: 0 AF XY: 0.0232 AC XY: 2899AN XY: 124962
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GnomAD4 genome ? AF: 0.0192 AC: 2917AN: 152254Hom.: 56 Cov.: 32 AF XY: 0.0182 AC XY: 1352AN XY: 74438
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
CYB561-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 22, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at