rs200870946

Variant names:

• chr20-53953448-C-A
• rs200870946
• NM_001366298.2:c.1799G>T

Your query was ambiguous. Multiple possible variants found:

• chr20-53953448-C-A
• chr20-53953448-C-T

Variant summary

Our verdict is Uncertain significance. The variant received 3 ACMG points: 3P and 0B. PM2 PP3

The NM_001366298.2(BCAS1):​c.1799G>T​(p.Gly600Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G600D) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 32)
• Consequence: BCAS1 NM_001366298.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.22
• Publications: 2 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: Uncertain_significance. The variant received 3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.781

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001366298.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BCAS1	NM_001366298.2	MANE Select	c.1799G>T	p.Gly600Val	missense	Exon 12 of 13	NP_001353227.1	A0A8I5KUN3
	BCAS1	NM_003657.4		c.1664G>T	p.Gly555Val	missense	Exon 11 of 12	NP_003648.2	O75363-1
	BCAS1	NM_001366295.2		c.1622G>T	p.Gly541Val	missense	Exon 10 of 11	NP_001353224.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BCAS1	ENST00000688948.1	MANE Select	c.1799G>T	p.Gly600Val	missense	Exon 12 of 13	ENSP00000508731.1	A0A8I5KUN3
	BCAS1	ENST00000395961.7	TSL:1	c.1664G>T	p.Gly555Val	missense	Exon 11 of 12	ENSP00000379290.3	O75363-1
	BCAS1	ENST00000371435.6	TSL:1	c.1430G>T	p.Gly477Val	missense	Exon 9 of 10	ENSP00000360490.2	G3XAF7

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.23
BayesDel_addAF	Pathogenic	0.27	D
BayesDel_noAF	Pathogenic	0.15
CADD	Uncertain	25
DANN	Uncertain	1.0
DEOGEN2	Benign	0.32	T
Eigen	Uncertain	0.65
Eigen_PC	Uncertain	0.62
FATHMM_MKL	Uncertain	0.92	D
LIST_S2	Uncertain	0.92	D
M_CAP	Uncertain	0.11	D
MetaRNN	Pathogenic	0.78	D
MetaSVM	Uncertain	-0.16	T
MutationAssessor	Uncertain	2.4	M
PhyloP100		3.2
PrimateAI	Benign	0.47	T
PROVEAN	Pathogenic	-8.2	D
REVEL	Uncertain	0.32
Sift	Uncertain	0.0030	D
Sift4G	Pathogenic	0.0	D
Polyphen		1.0	D
Vest4		0.76
MutPred		0.40		Gain of MoRF binding (P = 0.0904)
MVP		0.88
MPC		0.49
ClinPred		1.0	D
GERP RS		5.2
Varity_R		0.80
gMVP		0.14
Mutation Taster		=72/28	polymorphism

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: rs200870946; hg19: chr20-52569987;