chr1-61077852-CT-C
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2
The ENST00000371191.5(NFIA):c.97-10283del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00599 in 113,358 control chromosomes in the GnomAD database, including 1 homozygotes. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0060 ( 1 hom., cov: 31)
Consequence
NFIA
ENST00000371191.5 intron
ENST00000371191.5 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.959
Genes affected
NFIA (HGNC:7784): (nuclear factor I A) This gene encodes a member of the NF1 (nuclear factor 1) family of transcription factors. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2011]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP6
?
Variant 1-61077852-CT-C is Benign according to our data. Variant chr1-61077852-CT-C is described in ClinVar as [Likely_benign]. Clinvar id is 1214327.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00599 (679/113358) while in subpopulation AFR AF= 0.0165 (517/31302). AF 95% confidence interval is 0.0153. There are 1 homozygotes in gnomad4. There are 304 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
BS2
?
High AC in GnomAd at 680 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NFIA | NM_001145511.2 | c.3+238del | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NFIA | ENST00000371191.5 | c.97-10283del | intron_variant | 5 | |||||
NFIA | ENST00000407417.7 | c.3+238del | intron_variant | 2 | |||||
NFIA | ENST00000476646.5 | c.-114-10283del | intron_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.00600 AC: 680AN: 113376Hom.: 1 Cov.: 31
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?
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.00599 AC: 679AN: 113358Hom.: 1 Cov.: 31 AF XY: 0.00558 AC XY: 304AN XY: 54464
GnomAD4 genome
?
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Sep 08, 2019 | - - |
Computational scores
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Name
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Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at