7-73537310-C-G

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_Strong BP6_Moderate BP7 BS2

The NM_001707.4(BCL7B):c.597G>C(p.Ala199=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0036 in 1,614,024 control chromosomes in the GnomAD database, including 18 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.0023 (0 hom., cov: 32)
  • Exomes 𝑓: 0.0037 (18 hom.)
• Consequence: BCL7B NM_001707.4 synonymous
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -2.81

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]

ACMG classification

Verdict is Benign. Variant got -11 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BP6: Variant 7-73537310-C-G is Benign according to our data. Variant chr7-73537310-C-G is described in ClinVar as [Likely_benign]. Clinvar id is 2657554.Status of the report is criteria_provided_single_submitter, 1 stars.
• BP7: Synonymous conserved (PhyloP=-2.81 with no splicing effect.
• BS2: High Homozygotes in GnomAdExome4 at 18 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BCL7B	NM_001707.4	c.597G>C	p.Ala199=	synonymous_variant	6/6	ENST00000223368.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BCL7B	ENST00000223368.7	c.597G>C	p.Ala199=	synonymous_variant	6/6	1	NM_001707.4	P1

Frequencies

GnomAD3 genomes AF: 0.00231 AC: 351 AN: 152164 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.000627

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00105

Gnomad ASJ AF: 0.0130

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00145

Gnomad FIN AF: 0.00245

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.00320

Gnomad OTH AF: 0.00527

GnomAD3 exomes AF: 0.00289 AC: 724 AN: 250442 Hom.: 3 AF XY: 0.00287 AC XY: 389 AN XY: 135486

Gnomad AFR exome AF: 0.000431

Gnomad AMR exome AF: 0.00119

Gnomad ASJ exome AF: 0.0144

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00150

Gnomad FIN exome AF: 0.00319

Gnomad NFE exome AF: 0.00346

Gnomad OTH exome AF: 0.00425

GnomAD4 exome AF: 0.00373 AC: 5459 AN: 1461742 Hom.: 18 Cov.: 31 AF XY: 0.00375 AC XY: 2725 AN XY: 727174

Gnomad4 AFR exome AF: 0.000538

Gnomad4 AMR exome AF: 0.00134

Gnomad4 ASJ exome AF: 0.0152

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00141

Gnomad4 FIN exome AF: 0.00275

Gnomad4 NFE exome AF: 0.00398

Gnomad4 OTH exome AF: 0.00394

GnomAD4 genome AF: 0.00230 AC: 350 AN: 152282 Hom.: 0 Cov.: 32 AF XY: 0.00203 AC XY: 151 AN XY: 74472

Gnomad4 AFR AF: 0.000625

Gnomad4 AMR AF: 0.00105

Gnomad4 ASJ AF: 0.0130

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00124

Gnomad4 FIN AF: 0.00245

Gnomad4 NFE AF: 0.00321

Gnomad4 OTH AF: 0.00521

Alfa AF: 0.00281 Hom.: 0

Bravo AF: 0.00214

Asia WGS AF: 0.000577 AC: 2 AN: 3478

EpiCase AF: 0.00333

EpiControl AF: 0.00456

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Dec 01, 2022

BCL7B: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.018
DANN	Benign	0.51

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

Other links and lift over

dbSNP: rs142166738; hg19: chr7-72951640;