rs334725
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001134673.4(NFIA):c.559+55697G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.926 in 152,270 control chromosomes in the GnomAD database, including 65,512 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.93 ( 65512 hom., cov: 32)
Consequence
NFIA
NM_001134673.4 intron
NM_001134673.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.305
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 -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.949 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NFIA | NM_001134673.4 | c.559+55697G>A | intron_variant | ENST00000403491.8 | |||
NFIA | NM_001145511.2 | c.535+55697G>A | intron_variant | ||||
NFIA | NM_001145512.2 | c.694+55697G>A | intron_variant | ||||
NFIA | NM_005595.5 | c.559+55697G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NFIA | ENST00000403491.8 | c.559+55697G>A | intron_variant | 1 | NM_001134673.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.926 AC: 140941AN: 152152Hom.: 65457 Cov.: 32
GnomAD3 genomes
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.926 AC: 141055AN: 152270Hom.: 65512 Cov.: 32 AF XY: 0.929 AC XY: 69165AN XY: 74438
GnomAD4 genome
?
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141055
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152270
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32
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69165
AN XY:
74438
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3122
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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