chr6-105026441-C-T
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2
The NM_001004317.4(LIN28B):c.342C>T(p.Pro114=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000081 in 1,605,822 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.000066 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000083 ( 0 hom. )
Consequence
LIN28B
NM_001004317.4 synonymous
NM_001004317.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.717
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 -9 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.34).
BP6
?
Variant 6-105026441-C-T is Benign according to our data. Variant chr6-105026441-C-T is described in ClinVar as [Benign]. Clinvar id is 736009.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=0.717 with no splicing effect.
BS2
?
High AC in GnomAd at 10 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LIN28B | NM_001004317.4 | c.342C>T | p.Pro114= | synonymous_variant | 3/4 | ENST00000345080.5 | |
LIN28B | NM_001410939.1 | c.366C>T | p.Pro122= | synonymous_variant | 4/5 | ||
LIN28B | XM_006715477.3 | c.399C>T | p.Pro133= | synonymous_variant | 4/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LIN28B | ENST00000345080.5 | c.342C>T | p.Pro114= | synonymous_variant | 3/4 | 1 | NM_001004317.4 | P1 | |
LIN28B | ENST00000637759.1 | c.366C>T | p.Pro122= | synonymous_variant | 4/5 | 5 | |||
LIN28B | ENST00000635857.1 | c.399C>T | p.Pro133= | synonymous_variant | 5/6 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000658 AC: 10AN: 151930Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000434 AC: 106AN: 244296Hom.: 0 AF XY: 0.000280 AC XY: 37AN XY: 132214
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GnomAD4 exome AF: 0.0000825 AC: 120AN: 1453892Hom.: 0 Cov.: 29 AF XY: 0.0000650 AC XY: 47AN XY: 723260
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jun 26, 2018 | - - |
Computational 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
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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