rs13233571

chr7-73556901-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.648

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 -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/exons	MANE	UniProt
BCL7B	NM_001707.4	c.92+586G>A		intron_variant		ENST00000223368.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BCL7B	ENST00000223368.7	c.92+586G>A		intron_variant		1	NM_001707.4	P1

Frequencies

GnomAD3 genomes AF: 0.0922 AC: 14034 AN: 152150 Hom.: 761 Cov.: 32

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

Gnomad4 AFR exome AF: 0.0392

Gnomad4 AMR exome AF: 0.0585

Gnomad4 ASJ exome AF: 0.115

Gnomad4 EAS exome AF: 0.0864

Gnomad4 SAS exome AF: 0.0858

Gnomad4 FIN exome AF: 0.111

Gnomad4 NFE exome AF: 0.123

Gnomad4 OTH exome AF: 0.113

GnomAD4 genome AF: 0.0922 AC: 14041 AN: 152266 Hom.: 762 Cov.: 32 AF XY: 0.0920 AC XY: 6850 AN XY: 74458

Gnomad4 AFR AF: 0.0417

Gnomad4 AMR AF: 0.0716

Gnomad4 ASJ AF: 0.110

Gnomad4 EAS AF: 0.0997

Gnomad4 SAS AF: 0.0891

Gnomad4 FIN AF: 0.119

Gnomad4 NFE AF: 0.123

Gnomad4 OTH AF: 0.0900

Alfa AF: 0.115 Hom.: 1020

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
Dann	Benign	0.77

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: rs13233571; hg19: chr7-72971231;