Genetic Variant BCL7B:c.93-1396T>G (chr7-73553638-A-C) – ACMG Classification: Benign (-14 pts)

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2

The NM_001301061.2(BCL7B):c.35T>G(p.Val12Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00402 in 153,826 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 8/10 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0038 ( 2 hom., cov: 31)

Exomes 𝑓: 0.017 ( 0 hom. )

Consequence

BCL7B
NM_001301061.2 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.376

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 made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.005997807).

BP6

Variant 7-73553638-A-C is Benign according to our data. Variant chr7-73553638-A-C is described in ClinVar as [Likely_benign]. Clinvar id is 2657555.Status of the report is criteria_provided_single_submitter, 1 stars.

BS1

Variant frequency is greater than expected in population mid. gnomad4_exome allele frequency = 0.0173 (34/1960) while in subpopulation MID AF= 0.0234 (30/1284). AF 95% confidence interval is 0.0168. There are 0 homozygotes in gnomad4_exome. There are 17 alleles in male gnomad4_exome subpopulation. Median coverage is 0. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 2 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BCL7B	NM_001707.4 link	c.93-1396T>G		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.93-1396T>G		intron_variant	Intron 1 of 5	1	NM_001707.4	ENSP00000223368.2		Q9BQE9-1

Frequencies

GnomAD3 genomes

AF:

0.00387

AC:

587

AN:

151746

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00104

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00500

Gnomad ASJ

AF:

0.0110

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00979

Gnomad FIN

AF:

0.000662

Gnomad MID

AF:

0.0316

Gnomad NFE

AF:

0.00512

Gnomad OTH

AF:

0.00864

GnomAD4 exome

AF:

0.0173

AC:

AN:

1960

Hom.:

Cov.:

AF XY:

0.0166

AC XY:

AN XY:

1024

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.0156

Gnomad4 FIN exome

AF:

0.00478

Gnomad4 NFE exome

AF:

0.00

Gnomad4 OTH exome

AF:

0.00769

GnomAD4 genome

AF:

0.00385

AC:

584

AN:

151866

Hom.:

Cov.:

AF XY:

0.00372

AC XY:

276

AN XY:

74200

show subpopulations

Gnomad4 AFR

AF:

0.00104

Gnomad4 AMR

AF:

0.00499

Gnomad4 ASJ

AF:

0.0110

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00980

Gnomad4 FIN

AF:

0.000662

Gnomad4 NFE

AF:

0.00512

Gnomad4 OTH

AF:

0.00855

Alfa

AF:

0.000435

Hom.:

Bravo

AF:

0.00378

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

May 01, 2022

CeGaT Center for Human Genetics Tuebingen

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

BCL7B: BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.83

BayesDel_noAF

Benign

-0.97

CADD

Benign

5.1

DANN

Benign

0.63

DEOGEN2

Benign

0.39

FATHMM_MKL

Benign

0.0055

LIST_S2

Benign

0.57

MetaRNN

Benign

0.0060

Sift4G

Uncertain

0.0050

Vest4

0.24

MVP

0.26

GERP RS

0.43

gMVP

0.14

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over