chr11-298601-AGCAGCAGTGGCG-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 1P and 7B. PP3BP3BP6_ModerateBS2
The NM_001025295.3(IFITM5):c.287_298del(p.Pro96_Leu99del) variant causes a inframe deletion change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000434 in 1,613,510 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Benign (★). Synonymous variant affecting the same amino acid position (i.e. P96P) has been classified as Likely benign.
Frequency
Consequence
NM_001025295.3 inframe_deletion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IFITM5 | NM_001025295.3 | c.287_298del | p.Pro96_Leu99del | inframe_deletion | 2/2 | ENST00000382614.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IFITM5 | ENST00000382614.2 | c.287_298del | p.Pro96_Leu99del | inframe_deletion | 2/2 | 1 | NM_001025295.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000460 AC: 7AN: 152206Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000220 AC: 55AN: 250296Hom.: 0 AF XY: 0.000162 AC XY: 22AN XY: 135652
GnomAD4 exome AF: 0.0000431 AC: 63AN: 1461304Hom.: 0 AF XY: 0.0000330 AC XY: 24AN XY: 726954
GnomAD4 genome ? AF: 0.0000460 AC: 7AN: 152206Hom.: 0 Cov.: 33 AF XY: 0.0000538 AC XY: 4AN XY: 74348
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 12, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at