rs4711274
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001623.5(AIF1):c.25+35G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.135 in 1,612,118 control chromosomes in the GnomAD database, including 17,003 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 0.14 ( 1830 hom., cov: 31)
Exomes 𝑓: 0.13 ( 15173 hom. )
Consequence
AIF1
NM_001623.5 intron
NM_001623.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.341
Genes affected
AIF1 (HGNC:352): (allograft inflammatory factor 1) This gene encodes a protein that binds actin and calcium. This gene is induced by cytokines and interferon and may promote macrophage activation and growth of vascular smooth muscle cells and T-lymphocytes. Polymorphisms in this gene may be associated with systemic sclerosis. Alternative splicing results in multiple transcript variants, but the full-length and coding nature of some of these variants is not certain. [provided by RefSeq, Jan 2016]
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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=-0.85).
BA1
?
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.184 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AIF1 | NM_001623.5 | c.25+35G>A | intron_variant | ENST00000376059.8 | |||
AIF1 | NM_001318970.2 | c.-138+96G>A | intron_variant | ||||
AIF1 | XM_005248870.5 | c.25+35G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AIF1 | ENST00000376059.8 | c.25+35G>A | intron_variant | 1 | NM_001623.5 | P1 | |||
AIF1 | ENST00000337917.11 | c.67+96G>A | intron_variant | 1 | |||||
AIF1 | ENST00000466820.1 | n.75+35G>A | intron_variant, non_coding_transcript_variant | 5 | |||||
AIF1 | ENST00000497362.5 | n.77+96G>A | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.141 AC: 21424AN: 151958Hom.: 1826 Cov.: 31
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GnomAD3 exomes AF: 0.151 AC: 37856AN: 251180Hom.: 3594 AF XY: 0.143 AC XY: 19447AN XY: 135786
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GnomAD4 exome AF: 0.134 AC: 195719AN: 1460042Hom.: 15173 Cov.: 38 AF XY: 0.131 AC XY: 95384AN XY: 726414
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GnomAD4 genome ? AF: 0.141 AC: 21451AN: 152076Hom.: 1830 Cov.: 31 AF XY: 0.149 AC XY: 11061AN XY: 74344
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at