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GeneBe

7-73557563-C-G

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4

The NM_001707.4(BCL7B):c.16G>C(p.Val6Leu) variant causes a missense change. The variant allele was found at a frequency of 0.00000441 in 1,361,456 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.0000066 ( 0 hom., cov: 31)
Exomes 𝑓: 0.0000041 ( 0 hom. )

Consequence

BCL7B
NM_001707.4 missense

Scores

3
3
13

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 6.99
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]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 1 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.29234666).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
BCL7BNM_001707.4 linkuse as main transcriptc.16G>C p.Val6Leu missense_variant 1/6 ENST00000223368.7
BCL7BNM_001197244.2 linkuse as main transcriptc.16G>C p.Val6Leu missense_variant 1/5
BCL7BNM_001301061.2 linkuse as main transcriptc.-74G>C 5_prime_UTR_variant 1/7
BCL7BXM_047421029.1 linkuse as main transcriptc.-74G>C 5_prime_UTR_variant 1/6

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
BCL7BENST00000223368.7 linkuse as main transcriptc.16G>C p.Val6Leu missense_variant 1/61 NM_001707.4 P1Q9BQE9-1

Frequencies

GnomAD3 genomes
AF:
0.00000661
AC:
1
AN:
151400
Hom.:
0
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000148
Gnomad OTH
AF:
0.00
GnomAD4 exome
AF:
0.00000413
AC:
5
AN:
1210056
Hom.:
0
Cov.:
31
AF XY:
0.00000337
AC XY:
2
AN XY:
593200
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000512
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
AF:
0.00000661
AC:
1
AN:
151400
Hom.:
0
Cov.:
31
AF XY:
0.00
AC XY:
0
AN XY:
73964
show subpopulations
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000148
Gnomad4 OTH
AF:
0.00
Bravo
AF:
0.00000756

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 GeneticsMar 27, 2023The c.16G>C (p.V6L) alteration is located in exon 1 (coding exon 1) of the BCL7B gene. This alteration results from a G to C substitution at nucleotide position 16, causing the valine (V) at amino acid position 6 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
0.88
BayesDel_addAF
Benign
-0.14
T
BayesDel_noAF
Benign
-0.44
Cadd
Pathogenic
27
Dann
Uncertain
0.99
DEOGEN2
Benign
0.13
T;.
Eigen
Benign
-0.29
Eigen_PC
Benign
-0.30
FATHMM_MKL
Uncertain
0.89
D
LIST_S2
Uncertain
0.97
D;D
M_CAP
Pathogenic
0.42
D
MetaRNN
Benign
0.29
T;T
MetaSVM
Benign
-1.1
T
MutationAssessor
Benign
0.81
L;L
MutationTaster
Benign
1.0
D;D
PrimateAI
Pathogenic
0.90
D
PROVEAN
Benign
-1.7
N;N
REVEL
Benign
0.16
Sift
Benign
0.084
T;T
Sift4G
Benign
0.11
T;T
Polyphen
0.015
B;.
Vest4
0.21
MutPred
0.52
Loss of sheet (P = 0.0817);Loss of sheet (P = 0.0817);
MVP
0.32
MPC
1.4
ClinPred
0.91
D
GERP RS
2.5
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.8
Varity_R
0.27

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.

Other links and lift over

dbSNP: rs1295157268; hg19: chr7-72971893; API