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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107987166	XR_001748403.2	n.350-11633A>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02151	ENST00000815587.1	n.239-11633A>G		intron_variant	Intron 2 of 2
LINC02151	ENST00000815588.1	n.202-11633A>G		intron_variant	Intron 1 of 1
LINC02151	ENST00000815589.1	n.311-11633A>G		intron_variant	Intron 1 of 1

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 v4.3

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

Other links and lift over

dbSNP: rs12806755; hg19: chr11-116202789;