chr9-14088248-G-A
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Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2
The ENST00000543693.5(NFIB):c.879C>T(p.Tyr293=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000114 in 1,584,464 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00013 ( 1 hom., cov: 31)
Exomes 𝑓: 0.00011 ( 0 hom. )
Consequence
NFIB
ENST00000543693.5 synonymous
ENST00000543693.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.25
Genes affected
NFIB (HGNC:7785): (nuclear factor I B) Enables DNA-binding transcription activator activity, RNA polymerase II-specific; RNA polymerase II cis-regulatory region sequence-specific DNA binding activity; and transcription regulator inhibitor activity. Involved in brain development; negative regulation of DNA binding activity; and regulation of transcription by RNA polymerase II. Located in fibrillar center and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]
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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 (BayesDel_noAF=-0.36).
BP6
Variant 9-14088248-G-A is Benign according to our data. Variant chr9-14088248-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 3036950.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=1.25 with no splicing effect.
BS2
High AC in GnomAd4 at 20 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NFIB | NM_001190737.2 | c.*61C>T | 3_prime_UTR_variant | 11/11 | ENST00000380953.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NFIB | ENST00000380953.6 | c.*61C>T | 3_prime_UTR_variant | 11/11 | 1 | NM_001190737.2 |
Frequencies
GnomAD3 genomes AF: 0.000132 AC: 20AN: 151626Hom.: 1 Cov.: 31
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GnomAD3 exomes AF: 0.0000904 AC: 20AN: 221188Hom.: 0 AF XY: 0.000110 AC XY: 13AN XY: 118500
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GnomAD4 exome AF: 0.000112 AC: 161AN: 1432722Hom.: 0 Cov.: 31 AF XY: 0.000108 AC XY: 77AN XY: 710674
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GnomAD4 genome AF: 0.000132 AC: 20AN: 151742Hom.: 1 Cov.: 31 AF XY: 0.000148 AC XY: 11AN XY: 74140
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
NFIB-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Mar 02, 2023 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
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