Variant 2-218662282-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

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

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.797

Variant links:

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]

BCS1L links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 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_multiple_submitters_no_conflicts, 2 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 linkuse as main transcript	c.719+22C>T		intron_variant		ENST00000359273.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BCS1L	ENST00000359273.8 linkuse as main transcript	c.719+22C>T		intron_variant		1	NM_001079866.2	P1

Frequencies

GnomAD3 genomes

AF:

0.533

AC:

80953

AN:

151916

Hom.:

24751

Cov.:

show subpopulations

Gnomad AFR

AF:

0.852

Gnomad AMI

AF:

0.384

Gnomad AMR

AF:

0.447

Gnomad ASJ

AF:

0.400

Gnomad EAS

AF:

0.181

Gnomad SAS

AF:

0.325

Gnomad FIN

AF:

0.429

Gnomad MID

AF:

0.370

Gnomad NFE

AF:

0.427

Gnomad OTH

AF:

0.481

GnomAD3 exomes

AF:

0.419

AC:

105259

AN:

251422

Hom.:

24489

AF XY:

0.409

AC XY:

55613

AN XY:

135886

show subpopulations

Gnomad AFR exome

AF:

0.864

Gnomad AMR exome

AF:

0.403

Gnomad ASJ exome

AF:

0.390

Gnomad EAS exome

AF:

0.176

Gnomad SAS exome

AF:

0.332

Gnomad FIN exome

AF:

0.433

Gnomad NFE exome

AF:

0.422

Gnomad OTH exome

AF:

0.427

GnomAD4 exome

AF:

0.424

AC:

617165

AN:

1456700

Hom.:

136411

Cov.:

AF XY:

0.419

AC XY:

303649

AN XY:

725060

show subpopulations

Gnomad4 AFR exome

AF:

0.873

Gnomad4 AMR exome

AF:

0.408

Gnomad4 ASJ exome

AF:

0.395

Gnomad4 EAS exome

AF:

0.175

Gnomad4 SAS exome

AF:

0.331

Gnomad4 FIN exome

AF:

0.429

Gnomad4 NFE exome

AF:

0.427

Gnomad4 OTH exome

AF:

0.430

GnomAD4 genome

AF:

0.533

AC:

81080

AN:

152034

Hom.:

24818

Cov.:

AF XY:

0.525

AC XY:

39031

AN XY:

74306

show subpopulations

Gnomad4 AFR

AF:

0.852

Gnomad4 AMR

AF:

0.447

Gnomad4 ASJ

AF:

0.400

Gnomad4 EAS

AF:

0.182

Gnomad4 SAS

AF:

0.326

Gnomad4 FIN

AF:

0.429

Gnomad4 NFE

AF:

0.427

Gnomad4 OTH

AF:

0.481

Alfa

AF:

0.471

Hom.:

4844

Bravo

AF:

0.551

Asia WGS

AF:

0.300

AC:

1046

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 23, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

2.2

DANN

Benign

0.72

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over