rs1325432
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_005263.5(GFI1):c.*736C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.155 in 152,440 control chromosomes in the GnomAD database, including 2,055 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 0.16 ( 2047 hom., cov: 31)
Exomes 𝑓: 0.15 ( 8 hom. )
Consequence
GFI1
NM_005263.5 3_prime_UTR
NM_005263.5 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.385
Genes affected
GFI1 (HGNC:4237): (growth factor independent 1 transcriptional repressor) This gene encodes a nuclear zinc finger protein that functions as a transcriptional repressor. This protein plays a role in diverse developmental contexts, including hematopoiesis and oncogenesis. It functions as part of a complex along with other cofactors to control histone modifications that lead to silencing of the target gene promoters. Mutations in this gene cause autosomal dominant severe congenital neutropenia, and also dominant nonimmune chronic idiopathic neutropenia of adults, which are heterogeneous hematopoietic disorders that cause predispositions to leukemias and infections. Multiple alternatively spliced variants, encoding the same protein, have been identified for this gene. [provided by RefSeq, Jul 2008]
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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=-0.8).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.222 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GFI1 | NM_005263.5 | c.*736C>A | 3_prime_UTR_variant | 7/7 | ENST00000294702.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GFI1 | ENST00000294702.6 | c.*736C>A | 3_prime_UTR_variant | 7/7 | 2 | NM_005263.5 | P1 | ||
GFI1 | ENST00000370332.5 | c.*736C>A | 3_prime_UTR_variant | 7/7 | 1 | P1 | |||
GFI1 | ENST00000427103.6 | c.*736C>A | 3_prime_UTR_variant | 7/7 | 1 | P1 | |||
GFI1 | ENST00000696667.1 | c.*636C>A | 3_prime_UTR_variant | 2/2 |
Frequencies
GnomAD3 genomes ? AF: 0.156 AC: 23645AN: 151944Hom.: 2048 Cov.: 31
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GnomAD4 exome AF: 0.148 AC: 56AN: 378Hom.: 8 Cov.: 0 AF XY: 0.170 AC XY: 32AN XY: 188
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GnomAD4 genome ? AF: 0.155 AC: 23641AN: 152062Hom.: 2047 Cov.: 31 AF XY: 0.160 AC XY: 11883AN XY: 74322
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ClinVar
Not reported inComputational scores
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Name
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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