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. Variant got -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

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02458	ENST00000549278.2	n.157+67364C>T		intron_variant	Intron 1 of 6	4

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

Gnomad4 AFR AF: 0.196

Gnomad4 AMR AF: 0.175

Gnomad4 ASJ AF: 0.227

Gnomad4 EAS AF: 0.400

Gnomad4 SAS AF: 0.287

Gnomad4 FIN AF: 0.215

Gnomad4 NFE AF: 0.249

Gnomad4 OTH AF: 0.222

Alfa AF: 0.156 Hom.: 335

Bravo AF: 0.226

Asia WGS AF: 0.315 AC: 1097 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1091646; hg19: chr12-89635823;