14-104714221-C-T
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The NM_022489.4(INF2):c.3059C>T(p.Ala1020Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000846 in 1,547,822 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_022489.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
INF2 | NM_022489.4 | c.3059C>T | p.Ala1020Val | missense_variant | 21/23 | ENST00000392634.9 | NP_071934.3 | |
INF2 | NM_001031714.4 | c.3059C>T | p.Ala1020Val | missense_variant | 21/22 | NP_001026884.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
INF2 | ENST00000392634.9 | c.3059C>T | p.Ala1020Val | missense_variant | 21/23 | 5 | NM_022489.4 | ENSP00000376410.4 |
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152196Hom.: 0 Cov.: 35
GnomAD3 exomes AF: 0.0000345 AC: 6AN: 174068Hom.: 0 AF XY: 0.0000321 AC XY: 3AN XY: 93334
GnomAD4 exome AF: 0.0000881 AC: 123AN: 1395626Hom.: 0 Cov.: 31 AF XY: 0.0000844 AC XY: 58AN XY: 687510
GnomAD4 genome AF: 0.0000526 AC: 8AN: 152196Hom.: 0 Cov.: 35 AF XY: 0.0000404 AC XY: 3AN XY: 74348
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 15, 2020 | The p.A1020V variant (also known as c.3059C>T), located in coding exon 20 of the INF2 gene, results from a C to T substitution at nucleotide position 3059. The alanine at codon 1020 is replaced by valine, an amino acid with similar properties. This amino acid position is not well conserved in available vertebrate species, and valine is the reference amino acid in other vertebrate species. In addition, this alteration is predicted to be tolerated by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. - |
Focal segmental glomerulosclerosis 5;C4302667:Charcot-Marie-Tooth disease dominant intermediate E Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Mar 20, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at