ENST00000815587.1:n.238+32668A>G

Variant names:

• chr11-116446060-T-C
• rs489164
• ENST00000815587.1:n.238+32668A>G

Variant summary

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

The ENST00000815587.1(LINC02151):​n.238+32668A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.414 in 151,984 control chromosomes in the GnomAD database, including 13,512 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 0.41 (13512 hom., cov: 31)
• Consequence: LINC02151 ENST00000815587.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.115
• Publications: 0 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=-0.82).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.464 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02151	ENST00000815587.1		n.238+32668A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.414 AC: 62919 AN: 151866 Hom.: 13517 Cov.: 31

Gnomad AFR AF: 0.311

Gnomad AMI AF: 0.616

Gnomad AMR AF: 0.474

Gnomad ASJ AF: 0.529

Gnomad EAS AF: 0.414

Gnomad SAS AF: 0.278

Gnomad FIN AF: 0.536

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.446

Gnomad OTH AF: 0.412

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

GnomAD4 genome AF: 0.414 AC: 62926 AN: 151984 Hom.: 13512 Cov.: 31 AF XY: 0.418 AC XY: 31072 AN XY: 74284

African (AFR) AF: 0.311 AC: 12894 AN: 41452

American (AMR) AF: 0.473 AC: 7228 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.529 AC: 1836 AN: 3468

East Asian (EAS) AF: 0.414 AC: 2131 AN: 5152

South Asian (SAS) AF: 0.277 AC: 1330 AN: 4808

European-Finnish (FIN) AF: 0.536 AC: 5663 AN: 10562

Middle Eastern (MID) AF: 0.422 AC: 124 AN: 294

European-Non Finnish (NFE) AF: 0.446 AC: 30294 AN: 67956

Other (OTH) AF: 0.410 AC: 864 AN: 2108

Alfa AF: 0.434 Hom.: 48822

Bravo AF: 0.411

Asia WGS AF: 0.311 AC: 1084 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	9.0
DANN	Benign	0.80
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs489164; hg19: chr11-116316777;