dbSNP rs13233571: BCL7B:c.92+586G>A (chr7-73556901-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_001707.4(BCL7B):c.92+586G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.116 in 937,276 control chromosomes in the GnomAD database, including 6,696 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 0.092 ( 762 hom., cov: 32)

Exomes 𝑓: 0.12 ( 5934 hom. )

Consequence

BCL7B
NM_001707.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.648

Publications

56 publications found

Variant links:

Genes affected

BCL7B (HGNC:1005): (BAF chromatin remodeling complex subunit BCL7B) This gene encodes a member of the BCL7 family including BCL7A, BCL7B and BCL7C proteins. This member is BCL7B, which contains a region that is highly similar to the N-terminal segment of BCL7A or BCL7C proteins. The BCL7A protein is encoded by the gene known to be directly involved in a three-way gene translocation in a Burkitt lymphoma cell line. This gene is located at a chromosomal region commonly deleted in Williams syndrome. This gene is highly conserved from C. elegans to human. Multiple alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Oct 2010]

BCL7B 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=-0.86).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.12 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001707.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
BCL7B	NM_001707.4	MANE Select	c.92+586G>A	intron	N/A	NP_001698.2
BCL7B	NM_001301061.2		c.3+586G>A	intron	N/A	NP_001287990.1	F2Z3H6
BCL7B	NM_001197244.2		c.92+586G>A	intron	N/A	NP_001184173.1	Q9BQE9-4

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
BCL7B	ENST00000223368.7	TSL:1 MANE Select	c.92+586G>A	intron	N/A	ENSP00000223368.2	Q9BQE9-1
BCL7B	ENST00000945444.1		c.81+597G>A	intron	N/A	ENSP00000615503.1
BCL7B	ENST00000871802.1		c.92+586G>A	intron	N/A	ENSP00000541861.1

Frequencies

GnomAD3 genomes

AF:

0.0922

AC:

14034

AN:

152150

Hom.:

761

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0419

Gnomad AMI

AF:

0.0659

Gnomad AMR

AF:

0.0718

Gnomad ASJ

AF:

0.110

Gnomad EAS

AF:

0.0993

Gnomad SAS

AF:

0.0890

Gnomad FIN

AF:

0.119

Gnomad MID

AF:

0.123

Gnomad NFE

AF:

0.123

Gnomad OTH

AF:

0.0861

GnomAD4 exome

AF:

0.120

AC:

94340

AN:

785010

Hom.:

5934

AF XY:

0.120

AC XY:

43685

AN XY:

364210

show subpopulations

African (AFR)

AF:

0.0392

AC:

583

AN:

14874

American (AMR)

AF:

0.0585

AC:

AN:

1026

Ashkenazi Jewish (ASJ)

AF:

0.115

AC:

573

AN:

4978

East Asian (EAS)

AF:

0.0864

AC:

344

AN:

3982

South Asian (SAS)

AF:

0.0858

AC:

1323

AN:

15416

European-Finnish (FIN)

AF:

0.111

AC:

115

AN:

1032

Middle Eastern (MID)

AF:

0.113

AC:

176

AN:

1560

European-Non Finnish (NFE)

AF:

0.123

AC:

88263

AN:

716378

Other (OTH)

AF:

0.113

AC:

2903

AN:

25764

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

3792

7585

11377

15170

18962

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

4296

8592

12888

17184

21480

<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:

0.0922

AC:

14041

AN:

152266

Hom.:

762

Cov.:

AF XY:

0.0920

AC XY:

6850

AN XY:

74458

show subpopulations

African (AFR)

AF:

0.0417

AC:

1735

AN:

41558

American (AMR)

AF:

0.0716

AC:

1095

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.110

AC:

381

AN:

3468

East Asian (EAS)

AF:

0.0997

AC:

516

AN:

5176

South Asian (SAS)

AF:

0.0891

AC:

430

AN:

4828

European-Finnish (FIN)

AF:

0.119

AC:

1261

AN:

10612

Middle Eastern (MID)

AF:

0.122

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.123

AC:

8337

AN:

68012

Other (OTH)

AF:

0.0900

AC:

190

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

647

1294

1941

2588

3235

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

158

316

474

632

790

<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:

0.109

Hom.:

2529

Bravo

AF:

0.0841

Asia WGS

AF:

0.0960

AC:

335

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

5.6

(source)

DANN

Benign

0.77

PhyloP100

0.65

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