Menu
GeneBe

7-73543596-A-G

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_001707.4(BCL7B):c.217T>C(p.Phe73Leu) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 31)

Consequence

BCL7B
NM_001707.4 missense

Scores

2
4
13

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 6.18
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.21279967).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
BCL7BNM_001707.4 linkuse as main transcriptc.217T>C p.Phe73Leu missense_variant 3/6 ENST00000223368.7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
BCL7BENST00000223368.7 linkuse as main transcriptc.217T>C p.Phe73Leu missense_variant 3/61 NM_001707.4 P1Q9BQE9-1

Frequencies

GnomAD3 genomes
Cov.:
31
GnomAD4 exome
Cov.:
31
GnomAD4 genome
Cov.:
31

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingAmbry GeneticsAug 20, 2023The c.217T>C (p.F73L) alteration is located in exon 3 (coding exon 3) of the BCL7B gene. This alteration results from a T to C substitution at nucleotide position 217, causing the phenylalanine (F) at amino acid position 73 to be replaced by a leucine (L). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
0.74
BayesDel_addAF
Benign
-0.041
T
BayesDel_noAF
Benign
-0.30
Cadd
Benign
22
Dann
Uncertain
0.98
DEOGEN2
Benign
0.069
T;.;T
Eigen
Uncertain
0.49
Eigen_PC
Uncertain
0.54
FATHMM_MKL
Pathogenic
0.98
D
LIST_S2
Benign
0.82
T;T;D
M_CAP
Benign
0.0092
T
MetaRNN
Benign
0.21
T;T;T
MetaSVM
Benign
-0.98
T
MutationAssessor
Benign
1.8
L;L;.
MutationTaster
Benign
1.0
D;D
PrimateAI
Uncertain
0.72
T
PROVEAN
Benign
-0.96
N;N;.
REVEL
Benign
0.14
Sift
Benign
0.73
T;T;.
Sift4G
Benign
0.67
T;T;T
Polyphen
0.92
P;.;.
Vest4
0.37
MutPred
0.20
Loss of methylation at R68 (P = 0.1742);Loss of methylation at R68 (P = 0.1742);.;
MVP
0.41
MPC
0.70
ClinPred
0.91
D
GERP RS
5.4
Varity_R
0.080
gMVP
0.076

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.020
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr7-72957926; API