dbSNP rs11360: BCAN:c.*111A>G (chr1-156659245-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_021948.5(BCAN):c.*111A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.478 in 835,660 control chromosomes in the GnomAD database, including 97,064 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.50 ( 19289 hom., cov: 32)

Exomes 𝑓: 0.47 ( 77775 hom. )

Consequence

BCAN
NM_021948.5 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.673

Publications

16 publications found

Variant links:

Genes affected

BCAN (HGNC:23059): (brevican) This gene encodes a member of the lectican family of chondroitin sulfate proteoglycans that is specifically expressed in the central nervous system. This protein is developmentally regulated and may function in the formation of the brain extracellular matrix. This protein is highly expressed in gliomas and may promote the growth and cell motility of brain tumor cells. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Sep 2011]

BCAN links:

BCAN-AS2 (HGNC:56267): (BCAN antisense RNA 2)

BCAN-AS2 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.81).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.629 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_021948.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BCAN	NM_021948.5	MANE Select	c.*111A>G		3_prime_UTR	Exon 14 of 14	NP_068767.3
	BCAN-AS2	NR_182279.1		n.126+2070T>C		intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
BCAN	ENST00000329117.10	TSL:1 MANE Select	c.*111A>G	3_prime_UTR	Exon 14 of 14	ENSP00000331210.4	Q96GW7-1
BCAN	ENST00000884916.1		c.*111A>G	3_prime_UTR	Exon 14 of 14	ENSP00000554975.1
BCAN	ENST00000884917.1		c.*111A>G	3_prime_UTR	Exon 14 of 14	ENSP00000554976.1

Frequencies

GnomAD3 genomes

AF:

0.499

AC:

75693

AN:

151750

Hom.:

19248

Cov.:

show subpopulations

Gnomad AFR

AF:

0.595

Gnomad AMI

AF:

0.619

Gnomad AMR

AF:

0.437

Gnomad ASJ

AF:

0.540

Gnomad EAS

AF:

0.407

Gnomad SAS

AF:

0.649

Gnomad FIN

AF:

0.466

Gnomad MID

AF:

0.446

Gnomad NFE

AF:

0.453

Gnomad OTH

AF:

0.478

GnomAD4 exome

AF:

0.473

AC:

323466

AN:

683792

Hom.:

77775

Cov.:

AF XY:

0.480

AC XY:

167283

AN XY:

348862

show subpopulations

African (AFR)

AF:

0.607

AC:

9848

AN:

16218

American (AMR)

AF:

0.439

AC:

7927

AN:

18056

Ashkenazi Jewish (ASJ)

AF:

0.542

AC:

8320

AN:

15350

East Asian (EAS)

AF:

0.474

AC:

14710

AN:

31062

South Asian (SAS)

AF:

0.639

AC:

31388

AN:

49102

European-Finnish (FIN)

AF:

0.459

AC:

14676

AN:

31960

Middle Eastern (MID)

AF:

0.558

AC:

1448

AN:

2594

European-Non Finnish (NFE)

AF:

0.451

AC:

219001

AN:

485496

Other (OTH)

AF:

0.476

AC:

16148

AN:

33954

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

8576

17152

25728

34304

42880

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

4604

9208

13812

18416

23020

<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:

0.499

AC:

75790

AN:

151868

Hom.:

19289

Cov.:

AF XY:

0.499

AC XY:

37050

AN XY:

74198

show subpopulations

African (AFR)

AF:

0.595

AC:

24644

AN:

41390

American (AMR)

AF:

0.437

AC:

6680

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.540

AC:

1873

AN:

3470

East Asian (EAS)

AF:

0.406

AC:

2094

AN:

5158

South Asian (SAS)

AF:

0.648

AC:

3125

AN:

4822

European-Finnish (FIN)

AF:

0.466

AC:

4910

AN:

10544

Middle Eastern (MID)

AF:

0.442

AC:

130

AN:

294

European-Non Finnish (NFE)

AF:

0.453

AC:

30754

AN:

67900

Other (OTH)

AF:

0.483

AC:

1018

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1979

3957

5936

7914

9893

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

682

1364

2046

2728

3410

<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:

0.465

Hom.:

55841

Bravo

AF:

0.494

Asia WGS

AF:

0.546

AC:

1903

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

(source)

DANN

Benign

0.74

PhyloP100

0.67

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.060

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