20-54044202-T-C

Variant names:

• chr20-54044202-T-C
• rs2299700
• NM_001366298.2:c.142+13883A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
BCAS1	NM_001366298.2	c.142+13883A>G		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+13883A>G		intron_variant	Intron 3 of 12		NM_001366298.2	ENSP00000508731.1

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

African (AFR) AF: 0.0452 AC: 1877 AN: 41572

American (AMR) AF: 0.163 AC: 2496 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.157 AC: 546 AN: 3468

East Asian (EAS) AF: 0.142 AC: 738 AN: 5180

South Asian (SAS) AF: 0.147 AC: 707 AN: 4820

European-Finnish (FIN) AF: 0.209 AC: 2215 AN: 10592

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.166 AC: 11309 AN: 67992

Other (OTH) AF: 0.128 AC: 271 AN: 2110

Alfa AF: 0.151 Hom.: 2912

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
PhyloP100		-0.28
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2299700; hg19: chr20-52660741;