Variant chr17-61034748-A-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_ModerateBP6_ModerateBP7BS1BS2

The ENST00000407086.8(BCAS3):c.1720A>C(p.Arg574=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00689 in 1,612,952 control chromosomes in the GnomAD database, including 45 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0053 ( 1 hom., cov: 32)

Exomes 𝑓: 0.0071 ( 44 hom. )

Consequence

BCAS3
ENST00000407086.8 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 3.06

Variant links:

Genes affected

BCAS3 (HGNC:14347): (BCAS3 microtubule associated cell migration factor) Enables several functions, including acetyltransferase activator activity; beta-tubulin binding activity; and histone acetyltransferase binding activity. Involved in cellular response to estrogen stimulus; positive regulation of catalytic activity; and positive regulation of transcription by RNA polymerase II. Located in nucleus; phagophore assembly site; and transcriptionally active chromatin. Biomarker of breast cancer. [provided by Alliance of Genome Resources, Apr 2022]

BCAS3 links:

BCAS3-AS1 (HGNC:56376): (BCAS3 antisense RNA 1)

BCAS3-AS1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.26).

BP6

Variant 17-61034748-A-C is Benign according to our data. Variant chr17-61034748-A-C is described in ClinVar as [Likely_benign]. Clinvar id is 2647996.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=3.06 with no splicing effect.

BS1

Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.00529 (805/152308) while in subpopulation NFE AF= 0.0081 (551/68020). AF 95% confidence interval is 0.00754. There are 1 homozygotes in gnomad4. There are 411 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.

BS2

High Homozygotes in GnomAdExome4 at 44 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BCAS3	NM_017679.5 linkuse as main transcript	c.1720A>C	p.Arg574=	synonymous_variant	17/24	ENST00000407086.8	NP_060149.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BCAS3	ENST00000407086.8 linkuse as main transcript	c.1720A>C	p.Arg574=	synonymous_variant	17/24	1	NM_017679.5	ENSP00000385323	P3	Q9H6U6-2
BCAS3-AS1	ENST00000588604.1 linkuse as main transcript	n.317T>G		non_coding_transcript_exon_variant	3/3	5

Frequencies

GnomAD3 genomes

AF:

0.00529

AC:

805

AN:

152190

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00118

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00327

Gnomad ASJ

AF:

0.000576

Gnomad EAS

AF:

0.000193

Gnomad SAS

AF:

0.00352

Gnomad FIN

AF:

0.0121

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00810

Gnomad OTH

AF:

0.00334

GnomAD3 exomes

AF:

0.00481

AC:

1195

AN:

248578

Hom.:

AF XY:

0.00471

AC XY:

636

AN XY:

134894

show subpopulations

Gnomad AFR exome

AF:

0.000907

Gnomad AMR exome

AF:

0.00146

Gnomad ASJ exome

AF:

0.00120

Gnomad EAS exome

AF:

0.000112

Gnomad SAS exome

AF:

0.00211

Gnomad FIN exome

AF:

0.0110

Gnomad NFE exome

AF:

0.00692

Gnomad OTH exome

AF:

0.00563

GnomAD4 exome

AF:

0.00706

AC:

10307

AN:

1460644

Hom.:

Cov.:

AF XY:

0.00684

AC XY:

4971

AN XY:

726692

show subpopulations

Gnomad4 AFR exome

AF:

0.000808

Gnomad4 AMR exome

AF:

0.00123

Gnomad4 ASJ exome

AF:

0.000728

Gnomad4 EAS exome

AF:

0.0000252

Gnomad4 SAS exome

AF:

0.00177

Gnomad4 FIN exome

AF:

0.0107

Gnomad4 NFE exome

AF:

0.00818

Gnomad4 OTH exome

AF:

0.00640

GnomAD4 genome

AF:

0.00529

AC:

805

AN:

152308

Hom.:

Cov.:

AF XY:

0.00552

AC XY:

411

AN XY:

74476

show subpopulations

Gnomad4 AFR

AF:

0.00118

Gnomad4 AMR

AF:

0.00327

Gnomad4 ASJ

AF:

0.000576

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.00352

Gnomad4 FIN

AF:

0.0121

Gnomad4 NFE

AF:

0.00810

Gnomad4 OTH

AF:

0.00331

Alfa

AF:

0.00653

Hom.:

Bravo

AF:

0.00426

EpiCase

AF:

0.00736

EpiControl

AF:

0.00612

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Nov 01, 2022

BCAS3: BP4, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.26

CADD

Benign

DANN

Benign

0.68

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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