Genetic Variant BCAS3:c.2594-2637T>A (chr17-61389340-T-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_017679.5(BCAS3):c.2594-2637T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.592 in 152,532 control chromosomes in the GnomAD database, including 29,700 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 0.59 ( 29592 hom., cov: 33)

Exomes 𝑓: 0.69 ( 108 hom. )

Consequence

BCAS3
NM_017679.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.16

Publications

5 publications found

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:

TBX2-AS1 (HGNC:50355): (TBX2 antisense RNA 1)

TBX2-AS1 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.752 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BCAS3	NM_017679.5 link	c.2594-2637T>A		intron_variant	Intron 23 of 23	ENST00000407086.8	NP_060149.3	Q9H6U6-2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BCAS3	ENST00000407086.8 link	c.2594-2637T>A		intron_variant	Intron 23 of 23	1	NM_017679.5	ENSP00000385323.2		Q9H6U6-2

Frequencies

GnomAD3 genomes

AF:

0.592

AC:

89926

AN:

151992

Hom.:

29581

Cov.:

show subpopulations

Gnomad AFR

AF:

0.307

Gnomad AMI

AF:

0.793

Gnomad AMR

AF:

0.516

Gnomad ASJ

AF:

0.736

Gnomad EAS

AF:

0.467

Gnomad SAS

AF:

0.609

Gnomad FIN

AF:

0.734

Gnomad MID

AF:

0.643

Gnomad NFE

AF:

0.757

Gnomad OTH

AF:

0.593

GnomAD4 exome

AF:

0.690

AC:

291

AN:

422

Hom.:

108

Cov.:

AF XY:

0.694

AC XY:

179

AN XY:

258

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AF:

0.350

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AF:

0.786

AC:

AN:

European-Finnish (FIN)

AF:

0.750

AC:

AN:

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.726

AC:

241

AN:

332

Other (OTH)

AF:

0.567

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.525

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.591

AC:

89971

AN:

152110

Hom.:

29592

Cov.:

AF XY:

0.587

AC XY:

43677

AN XY:

74354

show subpopulations

African (AFR)

AF:

0.307

AC:

12733

AN:

41470

American (AMR)

AF:

0.516

AC:

7897

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.736

AC:

2554

AN:

3470

East Asian (EAS)

AF:

0.468

AC:

2411

AN:

5152

South Asian (SAS)

AF:

0.607

AC:

2928

AN:

4822

European-Finnish (FIN)

AF:

0.734

AC:

7776

AN:

10592

Middle Eastern (MID)

AF:

0.644

AC:

188

AN:

292

European-Non Finnish (NFE)

AF:

0.757

AC:

51507

AN:

68002

Other (OTH)

AF:

0.595

AC:

1254

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1676

3352

5028

6704

8380

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

732

1464

2196

2928

3660

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.667

Hom.:

4483

Bravo

AF:

0.562

Asia WGS

AF:

0.500

AC:

1743

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

0.54

(source)

DANN

Benign

0.49

PhyloP100

-1.2

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over