rs4983379
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_022489.4(INF2):c.2479C>A(p.Gln827Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000937 in 1,612,254 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_022489.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
INF2 | NM_022489.4 | c.2479C>A | p.Gln827Lys | missense_variant | 16/23 | ENST00000392634.9 | |
INF2 | NM_001031714.4 | c.2479C>A | p.Gln827Lys | missense_variant | 16/22 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
INF2 | ENST00000392634.9 | c.2479C>A | p.Gln827Lys | missense_variant | 16/23 | 5 | NM_022489.4 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.000138 AC: 21AN: 152184Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000511 AC: 126AN: 246386Hom.: 0 AF XY: 0.000327 AC XY: 44AN XY: 134354
GnomAD4 exome AF: 0.0000890 AC: 130AN: 1460070Hom.: 0 Cov.: 32 AF XY: 0.0000592 AC XY: 43AN XY: 726302
GnomAD4 genome ? AF: 0.000138 AC: 21AN: 152184Hom.: 0 Cov.: 33 AF XY: 0.000175 AC XY: 13AN XY: 74340
ClinVar
Submissions by phenotype
not specified Benign:1
Benign, no assertion criteria provided | clinical testing | Genetic Services Laboratory, University of Chicago | Aug 26, 2022 | - - |
Focal segmental glomerulosclerosis 5;C4302667:Charcot-Marie-Tooth disease dominant intermediate E Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 11, 2023 | - - |
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 15, 2021 | 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. - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 03, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at