rs9391253

Variant names:

• chr6-104919741-A-T
• rs9391253
• ENST00000636060.1:n.418+6843T>A

Variant summary

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

The ENST00000636060.1(LIN28B-AS1):​n.418+6843T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.294 in 151,824 control chromosomes in the GnomAD database, including 6,713 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 0.29 (6713 hom., cov: 31)
• Consequence: LIN28B-AS1 ENST00000636060.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.506
• Publications: 27 publications found

Genes affected

LIN28B-AS1 (HGNC:21553): (LIN28B antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.319 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LIN28B-AS1	ENST00000636060.1	n.418+6843T>A		intron_variant	Intron 3 of 3	5
LIN28B-AS1	ENST00000636951.1	n.458+6843T>A		intron_variant	Intron 3 of 4	5

Frequencies

GnomAD3 genomes AF: 0.294 AC: 44653 AN: 151706 Hom.: 6710 Cov.: 31

Gnomad AFR AF: 0.256

Gnomad AMI AF: 0.194

Gnomad AMR AF: 0.268

Gnomad ASJ AF: 0.282

Gnomad EAS AF: 0.304

Gnomad SAS AF: 0.271

Gnomad FIN AF: 0.321

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.322

Gnomad OTH AF: 0.282

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

GnomAD4 genome AF: 0.294 AC: 44667 AN: 151824 Hom.: 6713 Cov.: 31 AF XY: 0.296 AC XY: 21931 AN XY: 74184

African (AFR) AF: 0.256 AC: 10611 AN: 41412

American (AMR) AF: 0.268 AC: 4074 AN: 15212

Ashkenazi Jewish (ASJ) AF: 0.282 AC: 979 AN: 3472

East Asian (EAS) AF: 0.303 AC: 1563 AN: 5152

South Asian (SAS) AF: 0.272 AC: 1304 AN: 4796

European-Finnish (FIN) AF: 0.321 AC: 3378 AN: 10524

Middle Eastern (MID) AF: 0.344 AC: 101 AN: 294

European-Non Finnish (NFE) AF: 0.322 AC: 21892 AN: 67944

Other (OTH) AF: 0.279 AC: 588 AN: 2106

Alfa AF: 0.308 Hom.: 911

Bravo AF: 0.286

Asia WGS AF: 0.262 AC: 917 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	8.5
DANN	Benign	0.77
PhyloP100		0.51

Splicing

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

Other links and lift over

dbSNP: rs9391253; hg19: chr6-105367616;