rs10485311

Variant names:

• chr6-104890921-T-C
• rs10485311
• ENST00000636951.1:n.459-25834A>G

Variant summary

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

The ENST00000636951.1(LIN28B-AS1):​n.459-25834A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0545 in 152,236 control chromosomes in the GnomAD database, including 242 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 0.055 (242 hom., cov: 31)
• Consequence: LIN28B-AS1 ENST00000636951.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.901
• Publications: 2 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=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0702 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000636951.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LIN28B-AS1	ENST00000636951.1	TSL:5	n.459-25834A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0546 AC: 8311 AN: 152118 Hom.: 243 Cov.: 31

Gnomad AFR AF: 0.0428

Gnomad AMI AF: 0.0450

Gnomad AMR AF: 0.0429

Gnomad ASJ AF: 0.0524

Gnomad EAS AF: 0.0290

Gnomad SAS AF: 0.0772

Gnomad FIN AF: 0.0817

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0611

Gnomad OTH AF: 0.0506

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

GnomAD4 genome AF: 0.0545 AC: 8304 AN: 152236 Hom.: 242 Cov.: 31 AF XY: 0.0553 AC XY: 4119 AN XY: 74444

African (AFR) AF: 0.0427 AC: 1773 AN: 41544

American (AMR) AF: 0.0428 AC: 655 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0524 AC: 182 AN: 3472

East Asian (EAS) AF: 0.0287 AC: 149 AN: 5188

South Asian (SAS) AF: 0.0766 AC: 370 AN: 4828

European-Finnish (FIN) AF: 0.0817 AC: 866 AN: 10596

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0611 AC: 4152 AN: 67998

Other (OTH) AF: 0.0496 AC: 105 AN: 2116

Alfa AF: 0.0597 Hom.: 164

Bravo AF: 0.0509

Asia WGS AF: 0.0580 AC: 201 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.5
DANN	Benign	0.35
PhyloP100		0.90

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10485311;

hg19: chr6-105338796;