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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BCL7B	NM_001707.4 link	c.92+586G>A		intron_variant	Intron 1 of 5	ENST00000223368.7	NP_001698.2	Q9BQE9-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BCL7B	ENST00000223368.7 link	c.92+586G>A		intron_variant	Intron 1 of 5	1	NM_001707.4	ENSP00000223368.2		Q9BQE9-1

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 v4.3

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over