rs314277
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1
The NM_001004317.4(LIN28B):c.198+1501A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.787 in 152,012 control chromosomes in the GnomAD database, including 48,143 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 0.79 ( 48143 hom., cov: 32)
Consequence
LIN28B
NM_001004317.4 intron
NM_001004317.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.560
Genes affected
LIN28B (HGNC:32207): (lin-28 homolog B) The protein encoded by this gene belongs to the lin-28 family, which is characterized by the presence of a cold-shock domain and a pair of CCHC zinc finger domains. This gene is highly expressed in testis, fetal liver, placenta, and in primary human tumors and cancer cell lines. It is negatively regulated by microRNAs that target sites in the 3' UTR, and overexpression of this gene in primary tumors is linked to the repression of let-7 family of microRNAs and derepression of let-7 targets, which facilitates cellular transformation. [provided by RefSeq, Jun 2012]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.46).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.938 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LIN28B | NM_001004317.4 | c.198+1501A>C | intron_variant | ENST00000345080.5 | |||
LIN28B | NM_001410939.1 | c.222+1501A>C | intron_variant | ||||
LIN28B | XM_006715477.3 | c.255+1501A>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LIN28B | ENST00000345080.5 | c.198+1501A>C | intron_variant | 1 | NM_001004317.4 | P1 | |||
LIN28B | ENST00000635857.1 | c.255+1501A>C | intron_variant | 5 | |||||
LIN28B | ENST00000637759.1 | c.222+1501A>C | intron_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.787 AC: 119614AN: 151894Hom.: 48121 Cov.: 32
GnomAD3 genomes
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.787 AC: 119684AN: 152012Hom.: 48143 Cov.: 32 AF XY: 0.789 AC XY: 58614AN XY: 74314
GnomAD4 genome
?
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3070
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
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