Genetic Variant NM_017679.5:c.2593+10734C>T (chr17-61379228-C-T) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The NM_017679.5(BCAS3):c.2593+10734C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.691 in 152,070 control chromosomes in the GnomAD database, including 37,941 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 0.69 ( 37924 hom., cov: 32)

Exomes 𝑓: 0.83 ( 17 hom. )

Consequence

BCAS3
NM_017679.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.263

Publications

78 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 -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.42).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.811 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.2593+10734C>T	intron	N/A	NP_060149.3
BCAS3	NM_001353144.2		c.2728+10734C>T	intron	N/A	NP_001340073.1
BCAS3	NM_001330413.2		c.2639-1278C>T	intron	N/A	NP_001317342.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
BCAS3	ENST00000407086.8	TSL:1 MANE Select	c.2593+10734C>T	intron	N/A	ENSP00000385323.2
BCAS3	ENST00000390652.9	TSL:1	c.2638+10734C>T	intron	N/A	ENSP00000375067.4
BCAS3	ENST00000589222.5	TSL:1	c.2594-1278C>T	intron	N/A	ENSP00000466078.1

Frequencies

GnomAD3 genomes

AF:

0.691

AC:

105036

AN:

151898

Hom.:

37910

Cov.:

show subpopulations

Gnomad AFR

AF:

0.527

Gnomad AMI

AF:

0.908

Gnomad AMR

AF:

0.569

Gnomad ASJ

AF:

0.756

Gnomad EAS

AF:

0.484

Gnomad SAS

AF:

0.608

Gnomad FIN

AF:

0.804

Gnomad MID

AF:

0.709

Gnomad NFE

AF:

0.817

Gnomad OTH

AF:

0.682

GnomAD4 exome

AF:

0.827

AC:

AN:

Hom.:

Cov.:

AF XY:

0.857

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.500

AC:

AN:

American (AMR)

AF:

0.500

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

1.00

AC:

AN:

Middle Eastern (MID)

AF:

1.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.833

AC:

AN:

Other (OTH)

AF:

0.667

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.558

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:

0.691

AC:

105096

AN:

152018

Hom.:

37924

Cov.:

AF XY:

0.684

AC XY:

50835

AN XY:

74312

show subpopulations

African (AFR)

AF:

0.527

AC:

21815

AN:

41420

American (AMR)

AF:

0.570

AC:

8703

AN:

15272

Ashkenazi Jewish (ASJ)

AF:

0.756

AC:

2625

AN:

3470

East Asian (EAS)

AF:

0.484

AC:

2497

AN:

5160

South Asian (SAS)

AF:

0.607

AC:

2923

AN:

4816

European-Finnish (FIN)

AF:

0.804

AC:

8508

AN:

10588

Middle Eastern (MID)

AF:

0.704

AC:

207

AN:

294

European-Non Finnish (NFE)

AF:

0.817

AC:

55549

AN:

67978

Other (OTH)

AF:

0.684

AC:

1441

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1535

3070

4604

6139

7674

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

804

1608

2412

3216

4020

<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:

0.765

Hom.:

148842

Bravo

AF:

0.667

Asia WGS

AF:

0.551

AC:

1918

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.42

CADD

Benign

(source)

DANN

Benign

0.85

PhyloP100

0.26

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