rs1049200069
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_022489.4(INF2):c.610G>A(p.Val204Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000143 in 1,612,826 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 Benign (★).
Frequency
Consequence
NM_022489.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
INF2 | NM_022489.4 | c.610G>A | p.Val204Ile | missense_variant | 4/23 | ENST00000392634.9 | |
INF2 | NM_001031714.4 | c.610G>A | p.Val204Ile | missense_variant | 4/22 | ||
INF2 | NM_032714.3 | c.610G>A | p.Val204Ile | missense_variant | 4/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
INF2 | ENST00000392634.9 | c.610G>A | p.Val204Ile | missense_variant | 4/23 | 5 | NM_022489.4 | P4 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152240Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.00000402 AC: 1AN: 248760Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135300
GnomAD4 exome AF: 0.0000144 AC: 21AN: 1460586Hom.: 0 Cov.: 34 AF XY: 0.0000124 AC XY: 9AN XY: 726624
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152240Hom.: 0 Cov.: 34 AF XY: 0.00 AC XY: 0AN XY: 74372
ClinVar
Submissions by phenotype
Focal segmental glomerulosclerosis 5;C4302667:Charcot-Marie-Tooth disease dominant intermediate E Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 18, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at