9-16419369-T-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_017637.6(BNC2):c.2920A>G(p.Ile974Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0127 in 1,606,930 control chromosomes in the GnomAD database, including 177 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0090 ( 13 hom., cov: 31)
Exomes 𝑓: 0.013 ( 164 hom. )
Consequence
BNC2
NM_017637.6 missense
NM_017637.6 missense
Scores
2
16
Clinical Significance
Conservation
PhyloP100: 2.04
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 -14 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.0048466623).
BP6
?
Variant 9-16419369-T-C is Benign according to our data. Variant chr9-16419369-T-C is described in ClinVar as [Benign]. Clinvar id is 120240.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.00898 (1368/152270) while in subpopulation NFE AF= 0.016 (1090/68008). AF 95% confidence interval is 0.0152. There are 13 homozygotes in gnomad4. There are 632 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
BS2
?
High AC in GnomAd at 1368 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BNC2 | NM_017637.6 | c.2920A>G | p.Ile974Val | missense_variant | 7/7 | ENST00000380672.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BNC2 | ENST00000380672.9 | c.2920A>G | p.Ile974Val | missense_variant | 7/7 | 2 | NM_017637.6 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.00899 AC: 1368AN: 152152Hom.: 13 Cov.: 31
GnomAD3 genomes
?
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1368
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GnomAD3 exomes AF: 0.00878 AC: 2158AN: 245898Hom.: 16 AF XY: 0.00863 AC XY: 1145AN XY: 132654
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GnomAD4 exome AF: 0.0131 AC: 19096AN: 1454660Hom.: 164 Cov.: 35 AF XY: 0.0127 AC XY: 9206AN XY: 722756
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GnomAD4 genome ? AF: 0.00898 AC: 1368AN: 152270Hom.: 13 Cov.: 31 AF XY: 0.00849 AC XY: 632AN XY: 74458
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68
ESP6500AA
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15
ESP6500EA
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134
ExAC
?
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1106
Asia WGS
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4
AN:
3478
ClinVar
Significance: Benign
Submissions summary: Benign:1Other:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 26, 2024 | - - |
Hypotension Other:1
not provided, no classification provided | literature only | Centre for molecular medicine, Karolinska Institutet | - | - - |
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
Uncertain
D
LIST_S2
Benign
T;T
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationAssessor
Benign
L;.
MutationTaster
Benign
D;D;D
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N
REVEL
Benign
Sift
Benign
T;T
Sift4G
Benign
T;T
Polyphen
B;.
Vest4
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