chr9-16419487-G-A
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Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_017637.6(BNC2):c.2802C>T(p.Asp934=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000196 in 1,614,100 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 Benign (★).
Frequency
Genomes: 𝑓 0.000099 ( 0 hom., cov: 31)
Exomes 𝑓: 0.00021 ( 2 hom. )
Consequence
BNC2
NM_017637.6 synonymous
NM_017637.6 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.398
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 -11 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
BP6
Variant 9-16419487-G-A is Benign according to our data. Variant chr9-16419487-G-A is described in ClinVar as [Benign]. Clinvar id is 2907637.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.398 with no splicing effect.
BS2
High AC in GnomAd4 at 15 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BNC2 | NM_017637.6 | c.2802C>T | p.Asp934= | synonymous_variant | 7/7 | ENST00000380672.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BNC2 | ENST00000380672.9 | c.2802C>T | p.Asp934= | synonymous_variant | 7/7 | 2 | NM_017637.6 | P2 |
Frequencies
GnomAD3 genomes AF: 0.0000986 AC: 15AN: 152140Hom.: 0 Cov.: 31
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GnomAD3 exomes AF: 0.000458 AC: 115AN: 250880Hom.: 3 AF XY: 0.000649 AC XY: 88AN XY: 135608
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GnomAD4 exome AF: 0.000207 AC: 302AN: 1461842Hom.: 2 Cov.: 35 AF XY: 0.000294 AC XY: 214AN XY: 727224
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GnomAD4 genome AF: 0.0000985 AC: 15AN: 152258Hom.: 0 Cov.: 31 AF XY: 0.000161 AC XY: 12AN XY: 74444
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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 | Jan 02, 2023 | - - |
Computational scores
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Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at