Variant chr20-53953690-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2

The NM_001366298.2(BCAS1):c.1557A>G(p.Ser519=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00256 in 1,612,290 control chromosomes in the GnomAD database, including 86 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0032 ( 7 hom., cov: 32)

Exomes 𝑓: 0.0025 ( 79 hom. )

Consequence

BCAS1
NM_001366298.2 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -3.08

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 -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.95).

BP6

Variant 20-53953690-T-C is Benign according to our data. Variant chr20-53953690-T-C is described in ClinVar as [Benign]. Clinvar id is 770303.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-3.08 with no splicing effect.

BS1

Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.00321 (488/152178) while in subpopulation EAS AF= 0.03 (155/5162). AF 95% confidence interval is 0.0262. There are 7 homozygotes in gnomad4. There are 256 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 7 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BCAS1	NM_001366298.2 linkuse as main transcript	c.1557A>G	p.Ser519=	synonymous_variant	12/13	ENST00000688948.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BCAS1	ENST00000688948.1 linkuse as main transcript	c.1557A>G	p.Ser519=	synonymous_variant	12/13		NM_001366298.2	A2

Frequencies

GnomAD3 genomes

AF:

0.00320

AC:

487

AN:

152060

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000580

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0161

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.0300

Gnomad SAS

AF:

0.000414

Gnomad FIN

AF:

0.00331

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000235

Gnomad OTH

AF:

0.00479

GnomAD3 exomes

AF:

0.00695

AC:

1741

AN:

250444

Hom.:

AF XY:

0.00541

AC XY:

732

AN XY:

135394

show subpopulations

Gnomad AFR exome

AF:

0.000431

Gnomad AMR exome

AF:

0.0312

Gnomad ASJ exome

AF:

0.0000995

Gnomad EAS exome

AF:

0.0276

Gnomad SAS exome

AF:

0.000491

Gnomad FIN exome

AF:

0.00393

Gnomad NFE exome

AF:

0.000248

Gnomad OTH exome

AF:

0.00393

GnomAD4 exome

AF:

0.00249

AC:

3640

AN:

1460112

Hom.:

Cov.:

AF XY:

0.00221

AC XY:

1602

AN XY:

726132

show subpopulations

Gnomad4 AFR exome

AF:

0.000120

Gnomad4 AMR exome

AF:

0.0308

Gnomad4 ASJ exome

AF:

0.0000383

Gnomad4 EAS exome

AF:

0.0456

Gnomad4 SAS exome

AF:

0.000406

Gnomad4 FIN exome

AF:

0.00341

Gnomad4 NFE exome

AF:

0.0000999

Gnomad4 OTH exome

AF:

0.00216

GnomAD4 genome

AF:

0.00321

AC:

488

AN:

152178

Hom.:

Cov.:

AF XY:

0.00344

AC XY:

256

AN XY:

74396

show subpopulations

Gnomad4 AFR

AF:

0.000578

Gnomad4 AMR

AF:

0.0160

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.0300

Gnomad4 SAS

AF:

0.000621

Gnomad4 FIN

AF:

0.00331

Gnomad4 NFE

AF:

0.000235

Gnomad4 OTH

AF:

0.00474

Alfa

AF:

0.00113

Hom.:

Bravo

AF:

0.00466

Asia WGS

AF:

0.00635

AC:

AN:

3478

EpiCase

AF:

0.0000545

EpiControl

AF:

0.000119

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Mar 30, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

0.016

DANN

Benign

0.40

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over