dbSNP rs11079428: 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:

Genome browser will be placed here

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_017679.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
BCAS3	NM_017679.5	MANE Select	c.2594-2637T>A	intron	N/A	NP_060149.3
BCAS3	NM_001353144.2		c.2729-2637T>A	intron	N/A	NP_001340073.1
BCAS3	NM_001330413.2		c.2705-2637T>A	intron	N/A	NP_001317342.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
BCAS3	ENST00000407086.8	TSL:1 MANE Select	c.2594-2637T>A	intron	N/A	ENSP00000385323.2
BCAS3	ENST00000390652.9	TSL:1	c.2639-2637T>A	intron	N/A	ENSP00000375067.4
BCAS3	ENST00000589222.5	TSL:1	c.2750+632T>A	intron	N/A	ENSP00000466078.1

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 v4.9

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over