Variant chr20-53996010-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001366298.2(BCAS1):c.764G>A(p.Gly255Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0568 in 1,609,932 control chromosomes in the GnomAD database, including 6,358 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict 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 ( 2591 hom., cov: 32)

Exomes 𝑓: 0.050 ( 3767 hom. )

Consequence

BCAS1
NM_001366298.2 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.780

Variant links:

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]

BCAS1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0042648017).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.339 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BCAS1	NM_001366298.2 linkuse as main transcript	c.764G>A	p.Gly255Glu	missense_variant	5/13	ENST00000688948.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BCAS1	ENST00000688948.1 linkuse as main transcript	c.764G>A	p.Gly255Glu	missense_variant	5/13		NM_001366298.2	A2

Frequencies

GnomAD3 genomes

AF:

0.125

AC:

19055

AN:

152054

Hom.:

2584

Cov.:

show subpopulations

Gnomad AFR

AF:

0.344

Gnomad AMI

AF:

0.0110

Gnomad AMR

AF:

0.0576

Gnomad ASJ

AF:

0.0124

Gnomad EAS

AF:

0.0144

Gnomad SAS

AF:

0.0767

Gnomad FIN

AF:

0.0411

Gnomad MID

AF:

0.0696

Gnomad NFE

AF:

0.0416

Gnomad OTH

AF:

0.0909

GnomAD3 exomes

AF:

0.0629

AC:

15599

AN:

248188

Hom.:

1287

AF XY:

0.0598

AC XY:

8015

AN XY:

134120

show subpopulations

Gnomad AFR exome

AF:

0.352

Gnomad AMR exome

AF:

0.0358

Gnomad ASJ exome

AF:

0.0131

Gnomad EAS exome

AF:

0.0150

Gnomad SAS exome

AF:

0.0759

Gnomad FIN exome

AF:

0.0452

Gnomad NFE exome

AF:

0.0422

Gnomad OTH exome

AF:

0.0494

GnomAD4 exome

AF:

0.0497

AC:

72425

AN:

1457758

Hom.:

3767

Cov.:

AF XY:

0.0499

AC XY:

36172

AN XY:

725116

show subpopulations

Gnomad4 AFR exome

AF:

0.362

Gnomad4 AMR exome

AF:

0.0384

Gnomad4 ASJ exome

AF:

0.0125

Gnomad4 EAS exome

AF:

0.00964

Gnomad4 SAS exome

AF:

0.0759

Gnomad4 FIN exome

AF:

0.0450

Gnomad4 NFE exome

AF:

0.0405

Gnomad4 OTH exome

AF:

0.0631

GnomAD4 genome

AF:

0.125

AC:

19094

AN:

152174

Hom.:

2591

Cov.:

AF XY:

0.121

AC XY:

9018

AN XY:

74390

show subpopulations

Gnomad4 AFR

AF:

0.343

Gnomad4 AMR

AF:

0.0574

Gnomad4 ASJ

AF:

0.0124

Gnomad4 EAS

AF:

0.0144

Gnomad4 SAS

AF:

0.0767

Gnomad4 FIN

AF:

0.0411

Gnomad4 NFE

AF:

0.0416

Gnomad4 OTH

AF:

0.0900

Alfa

AF:

0.0544

Hom.:

1406

Bravo

AF:

0.136

TwinsUK

AF:

0.0410

AC:

152

ALSPAC

AF:

0.0348

AC:

134

ESP6500AA

AF:

0.338

AC:

1491

ESP6500EA

AF:

0.0409

AC:

352

ExAC

AF:

0.0707

AC:

8585

Asia WGS

AF:

0.0610

AC:

213

AN:

3478

EpiCase

AF:

0.0451

EpiControl

AF:

0.0426

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.076

BayesDel_addAF

Benign

-0.84

BayesDel_noAF

Benign

-0.84

CADD

Benign

1.2

DANN

Benign

0.52

DEOGEN2

Benign

0.014

T;.;T

Eigen

Benign

-1.4

Eigen_PC

Benign

-1.3

FATHMM_MKL

Benign

0.034

LIST_S2

Benign

0.60

T;T;T

MetaRNN

Benign

0.0043

T;T;T

MetaSVM

Benign

-0.93

MutationAssessor

Benign

-0.67

.;.;N

MutationTaster

Benign

1.0

P;P;P;P

PrimateAI

Benign

0.22

PROVEAN

Benign

-0.57

N;N;N

REVEL

Benign

0.049

Sift

Benign

1.0

T;T;T

Sift4G

Benign

1.0

T;T;T

Polyphen

0.0020, 0.0

.;B;B

Vest4

0.014, 0.039

MPC

0.11

ClinPred

0.00048

GERP RS

0.43

Varity_R

0.032

gMVP

0.026

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over