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GeneBe

7-73537310-C-G

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

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

Scores

2

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -2.81
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 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 GnomAdExome at 3 gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
BCL7BNM_001707.4 linkuse as main transcriptc.597G>C p.Ala199= synonymous_variant 6/6 ENST00000223368.7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
BCL7BENST00000223368.7 linkuse as main transcriptc.597G>C p.Ala199= synonymous_variant 6/61 NM_001707.4 P1Q9BQE9-1

Frequencies

GnomAD3 genomes
AF:
0.00231
AC:
351
AN:
152164
Hom.:
0
Cov.:
32
show subpopulations
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
show subpopulations
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
show subpopulations
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
show subpopulations
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
LINK: link

Submissions by phenotype

not provided Benign:1
Likely benign, criteria provided, single submitterclinical testingCeGaT Center for Human Genetics TuebingenDec 01, 2022BCL7B: 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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs142166738; hg19: chr7-72951640; API