11-122977658-G-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001098169.2(BSX):c.693C>A(p.His231Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00293 in 1,608,778 control chromosomes in the GnomAD database, including 102 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.015 ( 45 hom., cov: 33)
Exomes 𝑓: 0.0016 ( 57 hom. )
Consequence
BSX
NM_001098169.2 missense
NM_001098169.2 missense
Scores
3
15
Clinical Significance
Conservation
PhyloP100: 0.0250
Genes affected
BSX (HGNC:20450): (brain specific homeobox) Enables sequence-specific double-stranded DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to act upstream of or within several processes, including eating behavior; mammary gland involution; and positive regulation of transcription by RNA polymerase II. Predicted to be located in cytoplasm. Predicted to be part of chromatin. [provided by Alliance of Genome Resources, Apr 2022]
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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=0.002009511).
BP6
?
Variant 11-122977658-G-T is Benign according to our data. Variant chr11-122977658-G-T is described in ClinVar as [Benign]. Clinvar id is 768492.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0501 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BSX | NM_001098169.2 | c.693C>A | p.His231Gln | missense_variant | 3/3 | ENST00000343035.3 | |
LOC124902774 | XR_007062926.1 | downstream_gene_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BSX | ENST00000343035.3 | c.693C>A | p.His231Gln | missense_variant | 3/3 | 5 | NM_001098169.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0153 AC: 2328AN: 152192Hom.: 45 Cov.: 33
GnomAD3 genomes
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2328
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33
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GnomAD3 exomes AF: 0.00409 AC: 992AN: 242656Hom.: 23 AF XY: 0.00303 AC XY: 401AN XY: 132472
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GnomAD4 exome AF: 0.00164 AC: 2391AN: 1456468Hom.: 57 Cov.: 31 AF XY: 0.00141 AC XY: 1023AN XY: 724734
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GnomAD4 genome ? AF: 0.0153 AC: 2327AN: 152310Hom.: 45 Cov.: 33 AF XY: 0.0142 AC XY: 1057AN XY: 74484
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ESP6500AA
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178
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ExAC
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578
Asia WGS
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6
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3478
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jun 12, 2018 | - - |
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
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Benign
L
MutationTaster
Benign
D
PrimateAI
Benign
T
PROVEAN
Benign
N
REVEL
Uncertain
Sift
Benign
T
Sift4G
Uncertain
D
Polyphen
B
Vest4
MutPred
Loss of catalytic residue at L233 (P = 0.0783);
MVP
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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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