rs6598045
Variant names:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000526811.4(IFITM3):c.-23+223T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.182 in 647,542 control chromosomes in the GnomAD database, including 5,161 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.21 ( 1040 hom., cov: 32)
Exomes 𝑓: 0.18 ( 4121 hom. )
Consequence
IFITM3
ENST00000526811.4 intron
ENST00000526811.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.885
Genes affected
IFITM3 (HGNC:5414): (interferon induced transmembrane protein 3) Interferon-induced transmembrane (IFITM) proteins are a family of interferon induced antiviral proteins. The family contains five members, including IFITM1, IFITM2 and IFITM3 and belong to the CD225 superfamily. The protein encoded by this gene restricts cellular entry by diverse viral pathogens, such as influenza A virus, Ebola virus and Sars-CoV-2. [provided by RefSeq, Nov 2021]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.304 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ENSG00000251661 | ENST00000602429.1 | n.94+2255A>G | intron_variant | Intron 1 of 1 | 1 | |||||
IFITM3 | ENST00000526811.4 | c.-23+223T>C | intron_variant | Intron 1 of 2 | 5 | ENSP00000432108.1 | ||||
IFITM3 | ENST00000602735.2 | c.-22-229T>C | intron_variant | Intron 1 of 2 | 5 | ENSP00000473544.1 |
Frequencies
GnomAD3 genomes AF: 0.205 AC: 29273AN: 142876Hom.: 1042 Cov.: 32
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GnomAD4 exome AF: 0.176 AC: 88842AN: 504548Hom.: 4121 Cov.: 6 AF XY: 0.182 AC XY: 48045AN XY: 264384
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GnomAD4 genome AF: 0.205 AC: 29330AN: 142994Hom.: 1040 Cov.: 32 AF XY: 0.205 AC XY: 14350AN XY: 70018
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
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