rs11360

Variant names:

• chr1-156659245-A-G
• rs11360
• NM_021948.5:c.*111A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.673
• Publications: 16 publications found

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

ACMG classification

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BCAN	NM_021948.5	c.*111A>G		3_prime_UTR_variant	Exon 14 of 14	ENST00000329117.10	NP_068767.3
BCAN	XM_017002047.2	c.*111A>G		3_prime_UTR_variant	Exon 14 of 14		XP_016857536.1
BCAN	XM_011509866.1	c.*111A>G		3_prime_UTR_variant	Exon 14 of 14		XP_011508168.1
BCAN-AS2	NR_182279.1	n.126+2070T>C		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BCAN	ENST00000329117.10	c.*111A>G		3_prime_UTR_variant	Exon 14 of 14	1	NM_021948.5	ENSP00000331210.4

Frequencies

GnomAD3 genomes AF: 0.499 AC: 75693 AN: 151750 Hom.: 19248 Cov.: 32

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.: 9 AF XY: 0.480 AC XY: 167283 AN XY: 348862

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

GnomAD4 genome AF: 0.499 AC: 75790 AN: 151868 Hom.: 19289 Cov.: 32 AF XY: 0.499 AC XY: 37050 AN XY: 74198

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

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	11
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)

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

Other links and lift over

dbSNP: rs11360; hg19: chr1-156629037; COSMIC: COSV61260390;