rs2303561
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001079866.2(BCS1L):c.719+22C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.434 in 1,608,734 control chromosomes in the GnomAD database, including 161,229 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.53 ( 24818 hom., cov: 32)
Exomes 𝑓: 0.42 ( 136411 hom. )
Consequence
BCS1L
NM_001079866.2 intron
NM_001079866.2 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.797
Genes affected
BCS1L (HGNC:1020): (BCS1 homolog, ubiquinol-cytochrome c reductase complex chaperone) This gene encodes a homolog of the S. cerevisiae bcs1 protein which is involved in the assembly of complex III of the mitochondrial respiratory chain. The encoded protein does not contain a mitochondrial targeting sequence but experimental studies confirm that it is imported into mitochondria. Mutations in this gene are associated with mitochondrial complex III deficiency and the GRACILE syndrome. Several alternatively spliced transcripts encoding two different isoforms have been described. [provided by RefSeq, Jan 2016]
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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 2-218662282-C-T is Benign according to our data. Variant chr2-218662282-C-T is described in ClinVar as [Benign]. Clinvar id is 1291331.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.845 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BCS1L | NM_001079866.2 | c.719+22C>T | intron_variant | ENST00000359273.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BCS1L | ENST00000359273.8 | c.719+22C>T | intron_variant | 1 | NM_001079866.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.533 AC: 80953AN: 151916Hom.: 24751 Cov.: 32
GnomAD3 genomes
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GnomAD3 exomes AF: 0.419 AC: 105259AN: 251422Hom.: 24489 AF XY: 0.409 AC XY: 55613AN XY: 135886
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GnomAD4 exome AF: 0.424 AC: 617165AN: 1456700Hom.: 136411 Cov.: 35 AF XY: 0.419 AC XY: 303649AN XY: 725060
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GnomAD4 genome ? AF: 0.533 AC: 81080AN: 152034Hom.: 24818 Cov.: 32 AF XY: 0.525 AC XY: 39031AN XY: 74306
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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 | Jun 23, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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