rs76300431
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBS1BS2
The NM_001004317.4(LIN28B):c.-11C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000876 in 1,612,690 control chromosomes in the GnomAD database, including 8 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 0.0044 ( 3 hom., cov: 32)
Exomes 𝑓: 0.00050 ( 5 hom. )
Consequence
LIN28B
NM_001004317.4 5_prime_UTR
NM_001004317.4 5_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.73
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=-0.28).
BS1
Variant frequency is greater than expected in population afr. gnomad4_exome allele frequency = 0.000504 (736/1460466) while in subpopulation AFR AF= 0.0184 (616/33396). AF 95% confidence interval is 0.0172. There are 5 homozygotes in gnomad4_exome. There are 315 alleles in male gnomad4_exome subpopulation. Median coverage is 30. This position pass quality control queck.
BS2
High AC in GnomAd4 at 677 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LIN28B | NM_001004317.4 | c.-11C>T | 5_prime_UTR_variant | 1/4 | ENST00000345080.5 | ||
LIN28B | NM_001410939.1 | c.35-859C>T | intron_variant | ||||
LIN28B | XM_006715477.3 | c.68-859C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LIN28B | ENST00000345080.5 | c.-11C>T | 5_prime_UTR_variant | 1/4 | 1 | NM_001004317.4 | P1 | ||
LIN28B | ENST00000635857.1 | c.68-859C>T | intron_variant | 5 | |||||
LIN28B | ENST00000637759.1 | c.35-859C>T | intron_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.00444 AC: 675AN: 152106Hom.: 3 Cov.: 32
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GnomAD3 exomes AF: 0.00121 AC: 302AN: 250566Hom.: 2 AF XY: 0.000982 AC XY: 133AN XY: 135428
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GnomAD4 exome AF: 0.000504 AC: 736AN: 1460466Hom.: 5 Cov.: 30 AF XY: 0.000434 AC XY: 315AN XY: 726584
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GnomAD4 genome AF: 0.00445 AC: 677AN: 152224Hom.: 3 Cov.: 32 AF XY: 0.00434 AC XY: 323AN XY: 74450
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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
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at