rs2299700

chr20-54044202-T-Cchr20-54044202-T-G

Variant summary

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

The NM_001366298.2(BCAS1):c.142+13883A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.133 in 152,224 control chromosomes in the GnomAD database, including 1,585 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 0.13 (1585 hom., cov: 32)
• Consequence: BCAS1 NM_001366298.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.282

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=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.164 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BCAS1	NM_001366298.2	c.142+13883A>G		intron_variant		ENST00000688948.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BCAS1	ENST00000688948.1	c.142+13883A>G		intron_variant			NM_001366298.2	A2

Frequencies

GnomAD3 genomes AF: 0.133 AC: 20280 AN: 152106 Hom.: 1586 Cov.: 32

Gnomad AFR AF: 0.0451

Gnomad AMI AF: 0.100

Gnomad AMR AF: 0.163

Gnomad ASJ AF: 0.157

Gnomad EAS AF: 0.143

Gnomad SAS AF: 0.147

Gnomad FIN AF: 0.209

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.166

Gnomad OTH AF: 0.128

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

GnomAD4 genome AF: 0.133 AC: 20285 AN: 152224 Hom.: 1585 Cov.: 32 AF XY: 0.137 AC XY: 10189 AN XY: 74436

Gnomad4 AFR AF: 0.0452

Gnomad4 AMR AF: 0.163

Gnomad4 ASJ AF: 0.157

Gnomad4 EAS AF: 0.142

Gnomad4 SAS AF: 0.147

Gnomad4 FIN AF: 0.209

Gnomad4 NFE AF: 0.166

Gnomad4 OTH AF: 0.128

Alfa AF: 0.152 Hom.: 2338

Bravo AF: 0.126

Asia WGS AF: 0.155 AC: 542 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	2.9
Dann	Benign	0.74

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: rs2299700; hg19: chr20-52660741;