9-16419429-C-T
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_017637.6(BNC2):c.2860G>A(p.Ala954Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000435 in 1,607,898 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).
Frequency
Genomes: 𝑓 0.0000066 ( 0 hom., cov: 31)
Exomes 𝑓: 0.000047 ( 1 hom. )
Consequence
BNC2
NM_017637.6 missense
NM_017637.6 missense
Scores
19
Clinical Significance
Conservation
PhyloP100: 0.874
Genes affected
BNC2 (HGNC:30988): (basonuclin zinc finger protein 2) This gene encodes a conserved zinc finger protein. The encoded protein functions in skin color saturation. Mutations in this gene are associated with facial pigmented spots. This gene is also associated with susceptibility to adolescent idiopathic scoliosis. [provided by RefSeq, Jul 2016]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -9 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.025373816).
BP6
?
Variant 9-16419429-C-T is Benign according to our data. Variant chr9-16419429-C-T is described in ClinVar as [Benign]. Clinvar id is 870151.Status of the report is no_assertion_criteria_provided, 0 stars.
BS2
?
High AC in GnomAdExome at 20 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BNC2 | NM_017637.6 | c.2860G>A | p.Ala954Thr | missense_variant | 7/7 | ENST00000380672.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BNC2 | ENST00000380672.9 | c.2860G>A | p.Ala954Thr | missense_variant | 7/7 | 2 | NM_017637.6 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152182Hom.: 0 Cov.: 31
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GnomAD3 exomes AF: 0.0000813 AC: 20AN: 246026Hom.: 1 AF XY: 0.000136 AC XY: 18AN XY: 132702
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GnomAD4 exome AF: 0.0000474 AC: 69AN: 1455716Hom.: 1 Cov.: 35 AF XY: 0.0000774 AC XY: 56AN XY: 723624
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GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152182Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 1AN XY: 74338
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Amelogenesis imperfecta Benign:1
Benign, no assertion criteria provided | research | Institute of Human Genetics, University of Ulm | Apr 10, 2019 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
DEOGEN2
Benign
T;T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
D
LIST_S2
Benign
T;T
M_CAP
Benign
T
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationAssessor
Benign
L;.
MutationTaster
Benign
N;N;N
PrimateAI
Benign
T
PROVEAN
Benign
N;N
REVEL
Benign
Sift
Benign
T;T
Sift4G
Benign
T;T
Polyphen
B;.
Vest4
MutPred
Gain of phosphorylation at A954 (P = 0.0288);.;
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