chr11-116362681-C-T

Variant names:

• chr11-116362681-C-T
• rs10502215
• ENST00000815587.1:n.239-42242G>A

Variant summary

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

The ENST00000815587.1(LINC02151):​n.239-42242G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0462 in 152,234 control chromosomes in the GnomAD database, including 181 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 0.046 (181 hom., cov: 33)
• Consequence: LINC02151 ENST00000815587.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.20
• 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=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0789 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107987166	XR_001748403.2	n.350-42242G>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02151	ENST00000815587.1	n.239-42242G>A		intron_variant	Intron 2 of 2
LINC02151	ENST00000815588.1	n.202-42242G>A		intron_variant	Intron 1 of 1
LINC02151	ENST00000815589.1	n.310+23473G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0462 AC: 7024 AN: 152116 Hom.: 181 Cov.: 33

Gnomad AFR AF: 0.0472

Gnomad AMI AF: 0.0735

Gnomad AMR AF: 0.0274

Gnomad ASJ AF: 0.0499

Gnomad EAS AF: 0.00692

Gnomad SAS AF: 0.0846

Gnomad FIN AF: 0.0372

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0508

Gnomad OTH AF: 0.0484

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

GnomAD4 genome AF: 0.0462 AC: 7027 AN: 152234 Hom.: 181 Cov.: 33 AF XY: 0.0454 AC XY: 3376 AN XY: 74438

African (AFR) AF: 0.0471 AC: 1958 AN: 41536

American (AMR) AF: 0.0273 AC: 418 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0499 AC: 173 AN: 3468

East Asian (EAS) AF: 0.00713 AC: 37 AN: 5188

South Asian (SAS) AF: 0.0857 AC: 412 AN: 4808

European-Finnish (FIN) AF: 0.0372 AC: 394 AN: 10602

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0508 AC: 3454 AN: 68024

Other (OTH) AF: 0.0469 AC: 99 AN: 2110

Alfa AF: 0.0507 Hom.: 623

Bravo AF: 0.0440

Asia WGS AF: 0.0340 AC: 121 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.81
DANN	Benign	0.55
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs10502215; hg19: chr11-116233398;