rs490592

Variant names:

• chr11-116427650-A-C
• rs490592
• ENST00000815587.1:n.238+51078T>G

Your query was ambiguous. Multiple possible variants found:

• chr11-116427650-A-C
• chr11-116427650-A-G
• chr11-116427650-A-T

Variant summary

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

The ENST00000815587.1(LINC02151):​n.238+51078T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.803 in 152,014 control chromosomes in the GnomAD database, including 49,222 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 0.80 (49222 hom., cov: 30)
• Consequence: LINC02151 ENST00000815587.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.946
• Publications: 10 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.949 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107987166	XR_001748403.2	n.349+46227T>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02151	ENST00000815587.1	n.238+51078T>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.803 AC: 122013 AN: 151896 Hom.: 49169 Cov.: 30

Gnomad AFR AF: 0.749

Gnomad AMI AF: 0.631

Gnomad AMR AF: 0.826

Gnomad ASJ AF: 0.765

Gnomad EAS AF: 0.971

Gnomad SAS AF: 0.931

Gnomad FIN AF: 0.852

Gnomad MID AF: 0.766

Gnomad NFE AF: 0.807

Gnomad OTH AF: 0.768

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

GnomAD4 genome AF: 0.803 AC: 122125 AN: 152014 Hom.: 49222 Cov.: 30 AF XY: 0.809 AC XY: 60085 AN XY: 74294

African (AFR) AF: 0.750 AC: 31052 AN: 41430

American (AMR) AF: 0.826 AC: 12630 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.765 AC: 2652 AN: 3468

East Asian (EAS) AF: 0.971 AC: 5004 AN: 5152

South Asian (SAS) AF: 0.931 AC: 4484 AN: 4814

European-Finnish (FIN) AF: 0.852 AC: 9017 AN: 10584

Middle Eastern (MID) AF: 0.769 AC: 226 AN: 294

European-Non Finnish (NFE) AF: 0.807 AC: 54866 AN: 67968

Other (OTH) AF: 0.769 AC: 1620 AN: 2108

Alfa AF: 0.806 Hom.: 229337

Bravo AF: 0.796

Asia WGS AF: 0.928 AC: 3221 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.7
DANN	Benign	0.54
PhyloP100		-0.95

Splicing

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

Other links and lift over

dbSNP: rs490592; hg19: chr11-116298367;