Variant 2-218660612-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_001079866.2(BCS1L):c.-49-327C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.507 in 238,626 control chromosomes in the GnomAD database, including 35,067 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.47 ( 19742 hom., cov: 32)

Exomes 𝑓: 0.58 ( 15325 hom. )

Consequence

BCS1L
NM_001079866.2 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.182

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 -10 ACMG points.

BP6

Variant 2-218660612-C-T is Benign according to our data. Variant chr2-218660612-C-T is described in ClinVar as [Benign]. Clinvar id is 669695.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.798 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.-49-327C>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.-49-327C>T		intron_variant		1	NM_001079866.2	P1

Frequencies

GnomAD3 genomes

AF:

0.467

AC:

70944

AN:

151906

Hom.:

19743

Cov.:

show subpopulations

Gnomad AFR

AF:

0.148

Gnomad AMI

AF:

0.617

Gnomad AMR

AF:

0.553

Gnomad ASJ

AF:

0.600

Gnomad EAS

AF:

0.820

Gnomad SAS

AF:

0.675

Gnomad FIN

AF:

0.573

Gnomad MID

AF:

0.630

Gnomad NFE

AF:

0.573

Gnomad OTH

AF:

0.519

GnomAD4 exome

AF:

0.577

AC:

50003

AN:

86602

Hom.:

15325

Cov.:

AF XY:

0.587

AC XY:

26077

AN XY:

44388

show subpopulations

Gnomad4 AFR exome

AF:

0.127

Gnomad4 AMR exome

AF:

0.573

Gnomad4 ASJ exome

AF:

0.592

Gnomad4 EAS exome

AF:

0.827

Gnomad4 SAS exome

AF:

0.657

Gnomad4 FIN exome

AF:

0.566

Gnomad4 NFE exome

AF:

0.571

Gnomad4 OTH exome

AF:

0.566

GnomAD4 genome

AF:

0.467

AC:

70935

AN:

152024

Hom.:

19742

Cov.:

AF XY:

0.475

AC XY:

35284

AN XY:

74326

show subpopulations

Gnomad4 AFR

AF:

0.147

Gnomad4 AMR

AF:

0.554

Gnomad4 ASJ

AF:

0.600

Gnomad4 EAS

AF:

0.819

Gnomad4 SAS

AF:

0.674

Gnomad4 FIN

AF:

0.573

Gnomad4 NFE

AF:

0.573

Gnomad4 OTH

AF:

0.519

Alfa

AF:

0.508

Hom.:

2655

Bravo

AF:

0.449

Asia WGS

AF:

0.699

AC:

2429

AN:

3478

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 14, 2018

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

9.3

DANN

Benign

0.80

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.21

Details are displayed if max score is > 0.2

DS_AG_spliceai

0.21

Position offset: 23

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