7-73553638-A-C
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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
NM_001707.4 intron
Scores
1
8
Clinical Significance
Conservation
PhyloP100: 0.376
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 GnomAd4 at 2 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BCL7B | NM_001707.4 | c.93-1396T>G | intron_variant | ENST00000223368.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BCL7B | ENST00000223368.7 | c.93-1396T>G | intron_variant | 1 | NM_001707.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00387 AC: 587AN: 151746Hom.: 2 Cov.: 31
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GnomAD4 exome AF: 0.0173 AC: 34AN: 1960Hom.: 0 Cov.: 0 AF XY: 0.0166 AC XY: 17AN XY: 1024
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GnomAD4 genome AF: 0.00385 AC: 584AN: 151866Hom.: 2 Cov.: 31 AF XY: 0.00372 AC XY: 276AN XY: 74200
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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 submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | May 01, 2022 | BCL7B: BS2 - |
Computational scores
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Name
Calibrated prediction
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BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
DEOGEN2
Benign
T
FATHMM_MKL
Benign
N
LIST_S2
Benign
T
MetaRNN
Benign
T
MutationTaster
Benign
N;N
Sift4G
Uncertain
D
Vest4
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at