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GeneBe

7-73553638-A-C

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2

The NM_001707.4(BCL7B):c.93-1396T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00402 in 153,826 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0038 ( 2 hom., cov: 31)
Exomes 𝑓: 0.017 ( 0 hom. )

Consequence

BCL7B
NM_001707.4 intron

Scores

1
8

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.376
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 -14 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=0.005997807).
BP6
Variant 7-73553638-A-C is Benign according to our data. Variant chr7-73553638-A-C is described in ClinVar as [Likely_benign]. Clinvar id is 2657555.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
Variant frequency is greater than expected in population mid. gnomad4_exome allele frequency = 0.0173 (34/1960) while in subpopulation MID AF= 0.0234 (30/1284). AF 95% confidence interval is 0.0168. There are 0 homozygotes in gnomad4_exome. There are 17 alleles in male gnomad4_exome subpopulation. Median coverage is 0. This position pass quality control queck.
BS2
High Homozygotes in GnomAd at 2 gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
BCL7BNM_001707.4 linkuse as main transcriptc.93-1396T>G intron_variant ENST00000223368.7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
BCL7BENST00000223368.7 linkuse as main transcriptc.93-1396T>G intron_variant 1 NM_001707.4 P1Q9BQE9-1

Frequencies

GnomAD3 genomes
AF:
0.00387
AC:
587
AN:
151746
Hom.:
2
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.00104
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00500
Gnomad ASJ
AF:
0.0110
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00979
Gnomad FIN
AF:
0.000662
Gnomad MID
AF:
0.0316
Gnomad NFE
AF:
0.00512
Gnomad OTH
AF:
0.00864
GnomAD4 exome
AF:
0.0173
AC:
34
AN:
1960
Hom.:
0
Cov.:
0
AF XY:
0.0166
AC XY:
17
AN XY:
1024
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0156
Gnomad4 FIN exome
AF:
0.00478
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.00769
GnomAD4 genome
AF:
0.00385
AC:
584
AN:
151866
Hom.:
2
Cov.:
31
AF XY:
0.00372
AC XY:
276
AN XY:
74200
show subpopulations
Gnomad4 AFR
AF:
0.00104
Gnomad4 AMR
AF:
0.00499
Gnomad4 ASJ
AF:
0.0110
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00980
Gnomad4 FIN
AF:
0.000662
Gnomad4 NFE
AF:
0.00512
Gnomad4 OTH
AF:
0.00855
Alfa
AF:
0.000435
Hom.:
0
Bravo
AF:
0.00378

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 TuebingenMay 01, 2022BCL7B: BS2 -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
-0.83
T
BayesDel_noAF
Benign
-0.97
Cadd
Benign
5.1
Dann
Benign
0.63
DEOGEN2
Benign
0.39
T
FATHMM_MKL
Benign
0.0055
N
LIST_S2
Benign
0.57
T
MetaRNN
Benign
0.0060
T
MutationTaster
Benign
1.0
N;N
Sift4G
Uncertain
0.0050
D
Vest4
0.24
MVP
0.26
GERP RS
0.43
gMVP
0.14

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: rs150783798; hg19: chr7-72967968; API