11-298516-G-A
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Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_001025295.3(IFITM5):c.384C>T(p.Asp128Asp) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00138 in 1,611,422 control chromosomes in the GnomAD database, including 16 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.0017 ( 1 hom., cov: 33)
Exomes 𝑓: 0.0013 ( 15 hom. )
Consequence
IFITM5
NM_001025295.3 synonymous
NM_001025295.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -3.38
Genes affected
IFITM5 (HGNC:16644): (interferon induced transmembrane protein 5) This gene encodes a membrane protein thought to play a role in bone mineralization. This gene is located on chromosome 11 in a cluster of related genes which are induced by interferon, however, this gene has not been shown to be interferon inducible. A similar gene, located in a gene cluster on mouse chromosome 7, is a member of the interferon-inducible fragilis gene family. The mouse gene encodes a transmembrane protein described as participating in germ cell competence. A mutation in the 5' UTR of this gene has been associated with osteogenesis imperfecta type V (PMID: 22863190, 22863195). [provided by RefSeq, Aug 2012]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -17 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BP6
Variant 11-298516-G-A is Benign according to our data. Variant chr11-298516-G-A is described in ClinVar as [Benign]. Clinvar id is 741824.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=-3.38 with no splicing effect.
BS2
High AC in GnomAd4 at 252 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
IFITM5 | NM_001025295.3 | c.384C>T | p.Asp128Asp | synonymous_variant | 2/2 | ENST00000382614.2 | NP_001020466.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
IFITM5 | ENST00000382614.2 | c.384C>T | p.Asp128Asp | synonymous_variant | 2/2 | 1 | NM_001025295.3 | ENSP00000372059.2 |
Frequencies
GnomAD3 genomes AF: 0.00166 AC: 252AN: 152198Hom.: 1 Cov.: 33
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GnomAD3 exomes AF: 0.00231 AC: 575AN: 248650Hom.: 7 AF XY: 0.00210 AC XY: 283AN XY: 134988
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GnomAD4 exome AF: 0.00135 AC: 1967AN: 1459224Hom.: 15 Cov.: 31 AF XY: 0.00122 AC XY: 884AN XY: 725884
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GnomAD4 genome AF: 0.00166 AC: 252AN: 152198Hom.: 1 Cov.: 33 AF XY: 0.00215 AC XY: 160AN XY: 74348
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Osteogenesis imperfecta Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome Diagnostics Laboratory, The Hospital for Sick Children | Aug 12, 2020 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Dec 21, 2023 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at