rs221634
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001004317.4(LIN28B):c.*1430T>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.521 in 151,802 control chromosomes in the GnomAD database, including 21,762 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 0.52 ( 21694 hom., cov: 30)
Exomes 𝑓: 0.55 ( 68 hom. )
Consequence
LIN28B
NM_001004317.4 3_prime_UTR
NM_001004317.4 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.368
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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.617 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LIN28B | NM_001004317.4 | c.*1430T>A | 3_prime_UTR_variant | 4/4 | ENST00000345080.5 | ||
LIN28B | NM_001410939.1 | c.*1430T>A | 3_prime_UTR_variant | 5/5 | |||
LIN28B | XM_006715477.3 | c.*1430T>A | 3_prime_UTR_variant | 5/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LIN28B | ENST00000345080.5 | c.*1430T>A | 3_prime_UTR_variant | 4/4 | 1 | NM_001004317.4 | P1 | ||
LIN28B | ENST00000637759.1 | c.*1430T>A | 3_prime_UTR_variant | 5/5 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.521 AC: 78766AN: 151246Hom.: 21679 Cov.: 30
GnomAD3 genomes
?
AF:
AC:
78766
AN:
151246
Hom.:
Cov.:
30
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.546 AC: 239AN: 438Hom.: 68 Cov.: 0 AF XY: 0.538 AC XY: 143AN XY: 266
GnomAD4 exome
AF:
AC:
239
AN:
438
Hom.:
Cov.:
0
AF XY:
AC XY:
143
AN XY:
266
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.521 AC: 78800AN: 151364Hom.: 21694 Cov.: 30 AF XY: 0.518 AC XY: 38305AN XY: 73894
GnomAD4 genome
?
AF:
AC:
78800
AN:
151364
Hom.:
Cov.:
30
AF XY:
AC XY:
38305
AN XY:
73894
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
1971
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at