rs314262

Variant names:

• chr6-104946746-G-A
• rs314262
• NM_001410939.1:c.-15-3715G>A

Your query was ambiguous. Multiple possible variants found:

• chr6-104946746-G-A
• chr6-104946746-G-C
• chr6-104946746-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001410939.1(LIN28B):​c.-15-3715G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.47 in 151,992 control chromosomes in the GnomAD database, including 18,594 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 0.47 (18594 hom., cov: 33)
• Consequence: LIN28B NM_001410939.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.121
• Publications: 16 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.675 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001410939.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LIN28B	NM_001410939.1		c.-15-3715G>A		intron	N/A	NP_001397868.1	A0A1B0GVD3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LIN28B	ENST00000637759.1	TSL:5	c.-15-3715G>A		intron	N/A	ENSP00000490468.1	A0A1B0GVD3
	LIN28B	ENST00000635857.1	TSL:5	c.19-3715G>A		intron	N/A	ENSP00000489735.1	A0A1B0GTK2

Frequencies

GnomAD3 genomes AF: 0.471 AC: 71461 AN: 151874 Hom.: 18581 Cov.: 33

Gnomad AFR AF: 0.227

Gnomad AMI AF: 0.597

Gnomad AMR AF: 0.583

Gnomad ASJ AF: 0.578

Gnomad EAS AF: 0.694

Gnomad SAS AF: 0.592

Gnomad FIN AF: 0.559

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.545

Gnomad OTH AF: 0.528

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

GnomAD4 genome AF: 0.470 AC: 71494 AN: 151992 Hom.: 18594 Cov.: 33 AF XY: 0.474 AC XY: 35196 AN XY: 74250

African (AFR) AF: 0.227 AC: 9426 AN: 41484

American (AMR) AF: 0.583 AC: 8902 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.578 AC: 2007 AN: 3472

East Asian (EAS) AF: 0.694 AC: 3591 AN: 5174

South Asian (SAS) AF: 0.591 AC: 2844 AN: 4812

European-Finnish (FIN) AF: 0.559 AC: 5899 AN: 10550

Middle Eastern (MID) AF: 0.490 AC: 143 AN: 292

European-Non Finnish (NFE) AF: 0.545 AC: 37015 AN: 67926

Other (OTH) AF: 0.533 AC: 1125 AN: 2112

Alfa AF: 0.521 Hom.: 11639

Bravo AF: 0.464

Asia WGS AF: 0.651 AC: 2243 AN: 3452

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	9.1
DANN	Benign	0.76
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs314262; hg19: chr6-105394621;