rs17141154
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_002343.6(LTF):c.1057+77C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.179 in 1,499,612 control chromosomes in the GnomAD database, including 25,892 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 0.22 ( 4053 hom., cov: 32)
Exomes 𝑓: 0.17 ( 21839 hom. )
Consequence
LTF
NM_002343.6 intron
NM_002343.6 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -3.17
Genes affected
LTF (HGNC:6720): (lactotransferrin) This gene is a member of the transferrin family of genes and its protein product is found in the secondary granules of neutrophils. The protein is a major iron-binding protein in milk and body secretions with an antimicrobial activity, making it an important component of the non-specific immune system. The protein demonstrates a broad spectrum of properties, including regulation of iron homeostasis, host defense against a broad range of microbial infections, anti-inflammatory activity, regulation of cellular growth and differentiation and protection against cancer development and metastasis. Antimicrobial, antiviral, antifungal and antiparasitic activity has been found for this protein and its peptides. Activity against both DNA and RNA viruses has been found, including activity against SARS-CoV-2, and HIV. [provided by RefSeq, Jul 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=-0.96).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.328 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LTF | NM_002343.6 | c.1057+77C>T | intron_variant | ENST00000231751.9 | |||
LTF | NM_001199149.2 | c.925+77C>T | intron_variant | ||||
LTF | NM_001321121.2 | c.1057+77C>T | intron_variant | ||||
LTF | NM_001321122.2 | c.1018+77C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LTF | ENST00000231751.9 | c.1057+77C>T | intron_variant | 1 | NM_002343.6 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.218 AC: 33063AN: 151962Hom.: 4039 Cov.: 32
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GnomAD4 exome AF: 0.175 AC: 235676AN: 1347532Hom.: 21839 AF XY: 0.177 AC XY: 119080AN XY: 672176
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GnomAD4 genome ? AF: 0.218 AC: 33115AN: 152080Hom.: 4053 Cov.: 32 AF XY: 0.219 AC XY: 16266AN XY: 74334
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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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