rs1091646

Variant names:

• chr12-89242046-G-A
• rs1091646
• ENST00000549278.2:n.157+67364C>T

Your query was ambiguous. Multiple possible variants found:

• chr12-89242046-G-A
• chr12-89242046-G-T

Variant summary

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

The ENST00000549278.2(LINC02458):​n.157+67364C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.229 in 151,988 control chromosomes in the GnomAD database, including 4,140 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 0.23 (4140 hom., cov: 32)
• Consequence: LINC02458 ENST00000549278.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.73
• Publications: 2 publications found

Genes affected

LINC02458 (HGNC:53394): (long intergenic non-protein coding RNA 2458)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.386 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000549278.2. 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
	LINC02458	ENST00000549278.2	TSL:4	n.157+67364C>T		intron	N/A
	LINC02458	ENST00000846494.1		n.162+67364C>T		intron	N/A
	LINC02458	ENST00000846495.1		n.145-66772C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.229 AC: 34824 AN: 151868 Hom.: 4133 Cov.: 32

Gnomad AFR AF: 0.196

Gnomad AMI AF: 0.107

Gnomad AMR AF: 0.175

Gnomad ASJ AF: 0.227

Gnomad EAS AF: 0.400

Gnomad SAS AF: 0.287

Gnomad FIN AF: 0.215

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.249

Gnomad OTH AF: 0.222

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

GnomAD4 genome AF: 0.229 AC: 34860 AN: 151988 Hom.: 4140 Cov.: 32 AF XY: 0.230 AC XY: 17064 AN XY: 74294

African (AFR) AF: 0.196 AC: 8144 AN: 41470

American (AMR) AF: 0.175 AC: 2679 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.227 AC: 787 AN: 3466

East Asian (EAS) AF: 0.400 AC: 2064 AN: 5156

South Asian (SAS) AF: 0.287 AC: 1384 AN: 4822

European-Finnish (FIN) AF: 0.215 AC: 2274 AN: 10560

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.249 AC: 16887 AN: 67924

Other (OTH) AF: 0.222 AC: 470 AN: 2114

Alfa AF: 0.158 Hom.: 349

Bravo AF: 0.226

Asia WGS AF: 0.315 AC: 1097 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.40
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs1091646; hg19: chr12-89635823;