14-104714760-G-A
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP6BS1BS2
The NM_022489.4(INF2):c.3598G>A(p.Asp1200Asn) variant causes a missense change. The variant allele was found at a frequency of 0.0000369 in 1,599,530 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. D1200H) has been classified as Uncertain significance.
Frequency
Consequence
NM_022489.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
INF2 | NM_022489.4 | c.3598G>A | p.Asp1200Asn | missense_variant | 21/23 | ENST00000392634.9 | |
INF2 | NM_001031714.4 | c.3598G>A | p.Asp1200Asn | missense_variant | 21/22 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
INF2 | ENST00000392634.9 | c.3598G>A | p.Asp1200Asn | missense_variant | 21/23 | 5 | NM_022489.4 | P4 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152142Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.0000133 AC: 3AN: 226188Hom.: 0 AF XY: 0.00000803 AC XY: 1AN XY: 124556
GnomAD4 exome AF: 0.0000359 AC: 52AN: 1447388Hom.: 0 Cov.: 37 AF XY: 0.0000403 AC XY: 29AN XY: 719148
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152142Hom.: 0 Cov.: 34 AF XY: 0.0000135 AC XY: 1AN XY: 74308
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 07, 2023 | The c.3598G>A (p.D1200N) alteration is located in exon 21 (coding exon 20) of the INF2 gene. This alteration results from a G to A substitution at nucleotide position 3598, causing the aspartic acid (D) at amino acid position 1200 to be replaced by an asparagine (N). Based on insufficient or conflicting evidence, 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 | Invitae | Oct 04, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at