chr16-50354808-A-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_013263.5(BRD7):c.373T>A(p.Leu125Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000278 in 1,611,814 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.00049 ( 2 hom., cov: 33)
Exomes 𝑓: 0.00026 ( 0 hom. )
Consequence
BRD7
NM_013263.5 missense
NM_013263.5 missense
Scores
2
17
Clinical Significance
Conservation
PhyloP100: 1.65
Genes affected
BRD7 (HGNC:14310): (bromodomain containing 7) This gene encodes a protein which is a member of the bromodomain-containing protein family. The product of this gene has been identified as a component of one form of the SWI/SNF chromatin remodeling complex, and as a protein which interacts with p53 and is required for p53-dependent oncogene-induced senescence which prevents tumor growth. Pseudogenes have been described on chromosomes 2, 3, 6, 13 and 14. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.012723863).
BS2
?
High AC in GnomAd at 74 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BRD7 | NM_013263.5 | c.373T>A | p.Leu125Ile | missense_variant | 3/17 | ENST00000394688.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BRD7 | ENST00000394688.8 | c.373T>A | p.Leu125Ile | missense_variant | 3/17 | 1 | NM_013263.5 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.000486 AC: 74AN: 152210Hom.: 2 Cov.: 33
GnomAD3 genomes
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GnomAD3 exomes AF: 0.000311 AC: 78AN: 250670Hom.: 0 AF XY: 0.000266 AC XY: 36AN XY: 135512
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GnomAD4 exome AF: 0.000256 AC: 374AN: 1459486Hom.: 0 Cov.: 32 AF XY: 0.000253 AC XY: 184AN XY: 726056
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GnomAD4 genome ? AF: 0.000486 AC: 74AN: 152328Hom.: 2 Cov.: 33 AF XY: 0.000577 AC XY: 43AN XY: 74486
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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 submitter | clinical testing | Ambry Genetics | Sep 09, 2021 | The c.373T>A (p.L125I) alteration is located in exon 3 (coding exon 3) of the BRD7 gene. This alteration results from a T to A substitution at nucleotide position 373, causing the leucine (L) at amino acid position 125 to be replaced by an isoleucine (I). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
DEOGEN2
Benign
T;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T;T
M_CAP
Benign
T
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationAssessor
Benign
M;M
MutationTaster
Benign
D;D
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N
REVEL
Benign
Sift
Benign
T;T
Sift4G
Benign
T;T
Polyphen
B;P
Vest4
MVP
MPC
0.23
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
Splicing
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Calibrated prediction
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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