6-31616280-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_001623.5(AIF1):c.197-64C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000335 in 1,612,742 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001623.5 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
AIF1 | NM_001623.5 | c.197-64C>T | intron_variant | Intron 4 of 5 | ENST00000376059.8 | NP_001614.3 | ||
AIF1 | XM_005248870.5 | c.331C>T | p.Arg111Trp | missense_variant | Exon 4 of 4 | XP_005248927.1 | ||
AIF1 | NM_001318970.2 | c.35-64C>T | intron_variant | Intron 4 of 5 | NP_001305899.1 | |||
AIF1 | NM_032955.3 | c.35-64C>T | intron_variant | Intron 1 of 2 | NP_116573.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152068Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000203 AC: 5AN: 245974Hom.: 0 AF XY: 0.0000149 AC XY: 2AN XY: 134054
GnomAD4 exome AF: 0.0000342 AC: 50AN: 1460556Hom.: 0 Cov.: 36 AF XY: 0.0000275 AC XY: 20AN XY: 726580
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152186Hom.: 0 Cov.: 31 AF XY: 0.0000269 AC XY: 2AN XY: 74428
ClinVar
Submissions by phenotype
not specified Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at