rs13233571

Variant names:

• chr7-73556901-C-T
• rs13233571
• NM_001707.4:c.92+586G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 56 publications found

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

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	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.: 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

African (AFR) AF: 0.0392 AC: 583 AN: 14874

American (AMR) AF: 0.0585 AC: 60 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

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

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: 36 AN: 294

European-Non Finnish (NFE) AF: 0.123 AC: 8337 AN: 68012

Other (OTH) AF: 0.0900 AC: 190 AN: 2112

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
DANN	Benign	0.77
PhyloP100		0.65
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs13233571; hg19: chr7-72971231;