Variant rs314279 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The NM_001410939.1(LIN28B):c.34+3699C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.912 in 152,186 control chromosomes in the GnomAD database, including 63,429 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 0.91 ( 63429 hom., cov: 31)

Consequence

LIN28B
NM_001410939.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0240

Variant links:

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]

LIN28B links:

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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=-0.43).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.951 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LIN28B	NM_001410939.1 linkuse as main transcript	c.34+3699C>A		intron_variant			NP_001397868.1
LIN28B	XM_006715477.3 linkuse as main transcript	c.67+3699C>A		intron_variant			XP_006715540.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LIN28B	ENST00000635857.1 linkuse as main transcript	c.67+3699C>A		intron_variant		5		ENSP00000489735
LIN28B	ENST00000637759.1 linkuse as main transcript	c.34+3699C>A		intron_variant		5		ENSP00000490468

Frequencies

GnomAD3 genomes

AF:

0.912

AC:

138726

AN:

152068

Hom.:

63364

Cov.:

show subpopulations

Gnomad AFR

AF:

0.954

Gnomad AMI

AF:

0.956

Gnomad AMR

AF:

0.937

Gnomad ASJ

AF:

0.906

Gnomad EAS

AF:

0.973

Gnomad SAS

AF:

0.920

Gnomad FIN

AF:

0.868

Gnomad MID

AF:

0.975

Gnomad NFE

AF:

0.882

Gnomad OTH

AF:

0.920

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.912

AC:

138850

AN:

152186

Hom.:

63429

Cov.:

AF XY:

0.912

AC XY:

67855

AN XY:

74408

show subpopulations

Gnomad4 AFR

AF:

0.954

Gnomad4 AMR

AF:

0.937

Gnomad4 ASJ

AF:

0.906

Gnomad4 EAS

AF:

0.974

Gnomad4 SAS

AF:

0.920

Gnomad4 FIN

AF:

0.868

Gnomad4 NFE

AF:

0.882

Gnomad4 OTH

AF:

0.922

Alfa

AF:

0.902

Hom.:

44481

Bravo

AF:

0.920

Asia WGS

AF:

0.941

AC:

3271

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.43

CADD

Benign

9.6

DANN

Benign

0.56

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over