chr14-104701432-T-A
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_022489.4(INF2):c.67T>A(p.Ser23Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000965 in 1,596,232 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 Likely benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S23A) has been classified as Uncertain significance.
Frequency
Consequence
NM_022489.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
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.67T>A | p.Ser23Thr | missense_variant | 2/23 | ENST00000392634.9 | |
INF2 | NM_001031714.4 | c.67T>A | p.Ser23Thr | missense_variant | 2/22 | ||
INF2 | NM_032714.3 | c.67T>A | p.Ser23Thr | missense_variant | 2/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
INF2 | ENST00000392634.9 | c.67T>A | p.Ser23Thr | missense_variant | 2/23 | 5 | NM_022489.4 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000723 AC: 11AN: 152232Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000158 AC: 34AN: 215794Hom.: 0 AF XY: 0.000178 AC XY: 21AN XY: 118042
GnomAD4 exome AF: 0.0000990 AC: 143AN: 1444000Hom.: 0 Cov.: 31 AF XY: 0.000103 AC XY: 74AN XY: 716708
GnomAD4 genome ? AF: 0.0000723 AC: 11AN: 152232Hom.: 0 Cov.: 33 AF XY: 0.0000941 AC XY: 7AN XY: 74376
ClinVar
Submissions by phenotype
Focal segmental glomerulosclerosis 5;C4302667:Charcot-Marie-Tooth disease dominant intermediate E Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 05, 2024 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 24, 2020 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at