rs929271
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_002309.5(LIF):c.*1414A>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.262 in 152,200 control chromosomes in the GnomAD database, including 6,433 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 0.26 ( 6405 hom., cov: 31)
Exomes 𝑓: 0.29 ( 28 hom. )
Consequence
LIF
NM_002309.5 3_prime_UTR
NM_002309.5 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0570
Genes affected
LIF (HGNC:6596): (LIF interleukin 6 family cytokine) The protein encoded by this gene is a pleiotropic cytokine with roles in several different systems. It is involved in the induction of hematopoietic differentiation in normal and myeloid leukemia cells, induction of neuronal cell differentiation, regulator of mesenchymal to epithelial conversion during kidney development, and may also have a role in immune tolerance at the maternal-fetal interface. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Mar 2012]
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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=-0.83).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.441 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LIF | NM_002309.5 | c.*1414A>C | 3_prime_UTR_variant | 3/3 | ENST00000249075.4 | ||
LIF | NM_001257135.2 | c.*1577A>C | 3_prime_UTR_variant | 2/2 | |||
LIF | XM_047441361.1 | c.*1414A>C | 3_prime_UTR_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LIF | ENST00000249075.4 | c.*1414A>C | 3_prime_UTR_variant | 3/3 | 1 | NM_002309.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.263 AC: 39767AN: 151450Hom.: 6409 Cov.: 31
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GnomAD4 exome AF: 0.291 AC: 184AN: 632Hom.: 28 Cov.: 0 AF XY: 0.269 AC XY: 113AN XY: 420
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GnomAD4 genome ? AF: 0.262 AC: 39753AN: 151568Hom.: 6405 Cov.: 31 AF XY: 0.269 AC XY: 19926AN XY: 74070
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ClinVar
Not reported inComputational scores
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Name
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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