rs12806755

Variant names:

• chr11-116332072-T-C
• rs12806755
• ENST00000815587.1:n.239-11633A>G

Variant summary

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

The ENST00000815587.1(LINC02151):​n.239-11633A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0417 in 152,324 control chromosomes in the GnomAD database, including 184 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 0.042 (184 hom., cov: 33)
• Consequence: LINC02151 ENST00000815587.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.527
• Publications: 1 publications found

Genes affected

LINC02151 (HGNC:53013): (long intergenic non-protein coding RNA 2151)

LOC107987166 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 = 0.0584 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000815587.1. 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
	LINC02151	ENST00000815587.1		n.239-11633A>G		intron	N/A
	LINC02151	ENST00000815588.1		n.202-11633A>G		intron	N/A
	LINC02151	ENST00000815589.1		n.311-11633A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0418 AC: 6364 AN: 152206 Hom.: 184 Cov.: 33

Gnomad AFR AF: 0.0102

Gnomad AMI AF: 0.0537

Gnomad AMR AF: 0.0570

Gnomad ASJ AF: 0.0271

Gnomad EAS AF: 0.000963

Gnomad SAS AF: 0.0516

Gnomad FIN AF: 0.0461

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0600

Gnomad OTH AF: 0.0458

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

GnomAD4 genome AF: 0.0417 AC: 6359 AN: 152324 Hom.: 184 Cov.: 33 AF XY: 0.0415 AC XY: 3089 AN XY: 74478

African (AFR) AF: 0.0102 AC: 423 AN: 41584

American (AMR) AF: 0.0566 AC: 867 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.0271 AC: 94 AN: 3472

East Asian (EAS) AF: 0.000965 AC: 5 AN: 5180

South Asian (SAS) AF: 0.0518 AC: 250 AN: 4824

European-Finnish (FIN) AF: 0.0461 AC: 489 AN: 10618

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.0600 AC: 4080 AN: 68018

Other (OTH) AF: 0.0449 AC: 95 AN: 2116

Alfa AF: 0.0539 Hom.: 380

Bravo AF: 0.0395

Asia WGS AF: 0.0190 AC: 67 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	13
DANN	Benign	0.81
PhyloP100		0.53

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: rs12806755;

hg19: chr11-116202789;