rs290422

chr20-54048330-G-A

Variant summary

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

The NM_001366298.2(BCAS1):c.142+9755C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.144 in 152,044 control chromosomes in the GnomAD database, including 1,938 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 0.14 (1938 hom., cov: 32)
• Consequence: BCAS1 NM_001366298.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.796

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=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.239 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BCAS1	NM_001366298.2	c.142+9755C>T		intron_variant		ENST00000688948.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BCAS1	ENST00000688948.1	c.142+9755C>T		intron_variant			NM_001366298.2	A2

Frequencies

GnomAD3 genomes AF: 0.144 AC: 21900 AN: 151926 Hom.: 1941 Cov.: 32

Gnomad AFR AF: 0.0467

Gnomad AMI AF: 0.207

Gnomad AMR AF: 0.127

Gnomad ASJ AF: 0.255

Gnomad EAS AF: 0.109

Gnomad SAS AF: 0.251

Gnomad FIN AF: 0.157

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.193

Gnomad OTH AF: 0.151

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

GnomAD4 genome AF: 0.144 AC: 21896 AN: 152044 Hom.: 1938 Cov.: 32 AF XY: 0.145 AC XY: 10748 AN XY: 74314

Gnomad4 AFR AF: 0.0466

Gnomad4 AMR AF: 0.128

Gnomad4 ASJ AF: 0.255

Gnomad4 EAS AF: 0.109

Gnomad4 SAS AF: 0.250

Gnomad4 FIN AF: 0.157

Gnomad4 NFE AF: 0.193

Gnomad4 OTH AF: 0.149

Alfa AF: 0.186 Hom.: 3508

Bravo AF: 0.134

Asia WGS AF: 0.135 AC: 469 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	1.5
Dann	Benign	0.39

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: rs290422; hg19: chr20-52664869;