rs458990

Variant names:

• chr20-54056757-G-A
• rs458990
• NM_001366298.2:c.142+1328C>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001366298.2(BCAS1):​c.142+1328C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.71 in 152,088 control chromosomes in the GnomAD database, including 38,931 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 0.71 (38931 hom., cov: 31)
• Consequence: BCAS1 NM_001366298.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.543

Genes affected

BCAS1 (HGNC:974): (brain enriched myelin associated protein 1) This gene resides in a region at 20q13 which is amplified in a variety of tumor types and associated with more aggressive tumor phenotypes. Among the genes identified from this region, it was found to be highly expressed in three amplified breast cancer cell lines and in one breast tumor without amplification at 20q13.2. However, this gene is not in the common region of maximal amplification and its expression was not detected in the breast cancer cell line MCF7, in which this region is highly amplified. Although not consistently expressed, this gene is a candidate oncogene. [provided by RefSeq, Apr 2016]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.872 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BCAS1	NM_001366298.2	c.142+1328C>T		intron_variant	Intron 3 of 12	ENST00000688948.1	NP_001353227.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BCAS1	ENST00000688948.1	c.142+1328C>T		intron_variant	Intron 3 of 12		NM_001366298.2	ENSP00000508731.1

Frequencies

GnomAD3 genomes AF: 0.710 AC: 107914 AN: 151970 Hom.: 38861 Cov.: 31

Gnomad AFR AF: 0.800

Gnomad AMI AF: 0.583

Gnomad AMR AF: 0.641

Gnomad ASJ AF: 0.681

Gnomad EAS AF: 0.894

Gnomad SAS AF: 0.781

Gnomad FIN AF: 0.698

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.659

Gnomad OTH AF: 0.669

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.710 AC: 108044 AN: 152088 Hom.: 38931 Cov.: 31 AF XY: 0.715 AC XY: 53176 AN XY: 74360

Gnomad4 AFR AF: 0.800

Gnomad4 AMR AF: 0.641

Gnomad4 ASJ AF: 0.681

Gnomad4 EAS AF: 0.893

Gnomad4 SAS AF: 0.781

Gnomad4 FIN AF: 0.698

Gnomad4 NFE AF: 0.659

Gnomad4 OTH AF: 0.673

Alfa AF: 0.666 Hom.: 46325

Bravo AF: 0.706

Asia WGS AF: 0.833 AC: 2895 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.77
DANN	Benign	0.46

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

LitVar

Other links and lift over

dbSNP: rs458990; hg19: chr20-52673296;