Genetic Variant NM_001079866.2:c.1017T>C (chr2-218663143-T-C) – ACMG Classification: Benign (-19 pts)

Variant summary

Our verdict is Benign. The variant received -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BA1

The NM_001079866.2(BCS1L):c.1017T>C(p.Pro339Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0601 in 1,614,096 control chromosomes in the GnomAD database, including 8,930 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.15 ( 3979 hom., cov: 32)

Exomes 𝑓: 0.050 ( 4951 hom. )

Consequence

BCS1L
NM_001079866.2 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:12

Conservation

PhyloP100: 0.129

Publications

7 publications found

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 Gene-Disease associations (from GenCC):

Bjornstad syndrome
Inheritance: AR, AD Classification: DEFINITIVE, STRONG, MODERATE, SUPPORTIVE, LIMITED Submitted by: Labcorp Genetics (formerly Invitae), Orphanet, G2P, ClinGen, Ambry Genetics
GRACILE syndrome
Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Orphanet, Labcorp Genetics (formerly Invitae), G2P
mitochondrial complex III deficiency nuclear type 1
Inheritance: AR Classification: STRONG Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae)
mitochondrial complex III deficiency
Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
renal tubulopathy-encephalopathy-liver failure syndrome
Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
Leigh syndrome
Inheritance: AR Classification: LIMITED Submitted by: ClinGen

BCS1L links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -19 ACMG points.

BP4

Computational evidence support a benign effect (REVEL=0.017).

BP6

Variant 2-218663143-T-C is Benign according to our data. Variant chr2-218663143-T-C is described in ClinVar as Benign. ClinVar VariationId is 136505.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=0.129 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.424 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001079866.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
BCS1L	NM_001079866.2	MANE Select	c.1017T>C	p.Pro339Pro	synonymous	Exon 8 of 8	NP_001073335.1	Q9Y276
BCS1L	NM_001257342.2		c.1017T>C	p.Pro339Pro	synonymous	Exon 9 of 9	NP_001244271.1	Q9Y276
BCS1L	NM_001257343.2		c.1017T>C	p.Pro339Pro	synonymous	Exon 9 of 9	NP_001244272.1	A0A024R445

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
BCS1L	ENST00000359273.8	TSL:1 MANE Select	c.1017T>C	p.Pro339Pro	synonymous	Exon 8 of 8	ENSP00000352219.3	Q9Y276
BCS1L	ENST00000392109.5	TSL:1	c.1017T>C	p.Pro339Pro	synonymous	Exon 9 of 9	ENSP00000375957.1	Q9Y276
BCS1L	ENST00000392111.7	TSL:1	c.1017T>C	p.Pro339Pro	synonymous	Exon 9 of 9	ENSP00000375959.2	Q9Y276

Frequencies

GnomAD3 genomes

AF:

0.152

AC:

23109

AN:

152092

Hom.:

3958

Cov.:

show subpopulations

Gnomad AFR

AF:

0.429

Gnomad AMI

AF:

0.0230

Gnomad AMR

AF:

0.0740

Gnomad ASJ

AF:

0.0493

Gnomad EAS

AF:

0.119

Gnomad SAS

AF:

0.0526

Gnomad FIN

AF:

0.0277

Gnomad MID

AF:

0.108

Gnomad NFE

AF:

0.0379

Gnomad OTH

AF:

0.126

GnomAD2 exomes

AF:

0.0717

AC:

18033

AN:

251388

AF XY:

0.0645

show subpopulations

Gnomad AFR exome

AF:

0.435

Gnomad AMR exome

AF:

0.0417

Gnomad ASJ exome

AF:

0.0466

Gnomad EAS exome

AF:

0.115

Gnomad FIN exome

AF:

0.0320

Gnomad NFE exome

AF:

0.0379

Gnomad OTH exome

AF:

0.0614

GnomAD4 exome

AF:

0.0505

AC:

73763

AN:

1461886

Hom.:

4951

Cov.:

AF XY:

0.0495

AC XY:

36014

AN XY:

727248

show subpopulations

African (AFR)

AF:

0.453

AC:

15151

AN:

33480

American (AMR)

AF:

0.0451

AC:

2019

AN:

44722

Ashkenazi Jewish (ASJ)

AF:

0.0494

AC:

1291

AN:

26136

East Asian (EAS)

AF:

0.113

AC:

4469

AN:

39700

South Asian (SAS)

AF:

0.0501

AC:

4319

AN:

86258

European-Finnish (FIN)

AF:

0.0317

AC:

1695

AN:

53420

Middle Eastern (MID)

AF:

0.0740

AC:

427

AN:

5768

European-Non Finnish (NFE)

AF:

0.0360

AC:

40079

AN:

1112008

Other (OTH)

AF:

0.0714

AC:

4313

AN:

60394

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.478

Heterozygous variant carriers

4859

9718

14576

19435

24294

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1762

3524

5286

7048

8810

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.152

AC:

23191

AN:

152210

Hom.:

3979

Cov.:

AF XY:

0.148

AC XY:

11000

AN XY:

74430

show subpopulations

African (AFR)

AF:

0.430

AC:

17821

AN:

41488

American (AMR)

AF:

0.0740

AC:

1133

AN:

15304

Ashkenazi Jewish (ASJ)

AF:

0.0493

AC:

171

AN:

3468

East Asian (EAS)

AF:

0.120

AC:

620

AN:

5176

South Asian (SAS)

AF:

0.0531

AC:

256

AN:

4822

European-Finnish (FIN)

AF:

0.0277

AC:

294

AN:

10624

Middle Eastern (MID)

AF:

0.122

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0379

AC:

2575

AN:

68010

Other (OTH)

AF:

0.125

AC:

264

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

771

1542

2312

3083

3854

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

212

424

636

848

1060

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0848

Hom.:

866

Bravo

AF:

0.168

Asia WGS

AF:

0.0960

AC:

333

AN:

3478

EpiCase

AF:

0.0401

EpiControl

AF:

0.0417

ClinVar

ClinVar submissions

Significance:Benign

Revision:criteria provided, multiple submitters, no conflicts

View on ClinVar

Pathogenic

VUS

Benign

Condition

GRACILE syndrome (3)

not provided (3)

Mitochondrial complex III deficiency nuclear type 1 (2)

not specified (2)

Leigh syndrome (1)

Pili torti-deafness syndrome (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.65

CADD

Benign

7.9

(source)

DANN

Benign

0.58

PhyloP100

0.13

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Mutation Taster

=88/12

polymorphism (auto)

(source)

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over