chr1-156659245-A-G

Position:

• chr1-156659245-A-G

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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/exons	MANE	UniProt
BCAN	NM_021948.5	c.*111A>G		3_prime_UTR_variant	14/14	ENST00000329117.10
BCAN-AS2	NR_182279.1	n.126+2070T>C		intron_variant, non_coding_transcript_variant
BCAN	XM_011509866.1	c.*111A>G		3_prime_UTR_variant	14/14
BCAN	XM_017002047.2	c.*111A>G		3_prime_UTR_variant	14/14

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BCAN	ENST00000329117.10	c.*111A>G		3_prime_UTR_variant	14/14	1	NM_021948.5	P1
BCAN-AS2	ENST00000448869.1	n.110+2070T>C		intron_variant, non_coding_transcript_variant		2
BCAN	ENST00000496038.1	n.1584A>G		non_coding_transcript_exon_variant	4/4	2

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

Gnomad4 AFR exome AF: 0.607

Gnomad4 AMR exome AF: 0.439

Gnomad4 ASJ exome AF: 0.542

Gnomad4 EAS exome AF: 0.474

Gnomad4 SAS exome AF: 0.639

Gnomad4 FIN exome AF: 0.459

Gnomad4 NFE exome AF: 0.451

Gnomad4 OTH exome AF: 0.476

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

Gnomad4 AFR AF: 0.595

Gnomad4 AMR AF: 0.437

Gnomad4 ASJ AF: 0.540

Gnomad4 EAS AF: 0.406

Gnomad4 SAS AF: 0.648

Gnomad4 FIN AF: 0.466

Gnomad4 NFE AF: 0.453

Gnomad4 OTH AF: 0.483

Alfa AF: 0.460 Hom.: 22201

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
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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

LitVar

Other links and lift over

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