ENST00000419151.2:n.232G>A

Variant names:

• chr17-16988951-G-A
• rs9907308
• ENST00000419151.2:n.232G>A

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000419151.2(LINC02090):​n.232G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.364 in 471,028 control chromosomes in the GnomAD database, including 32,387 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 0.38 (11658 hom., cov: 32)
  • Exomes 𝑓: 0.36 (20729 hom.)
• Consequence: LINC02090 ENST00000419151.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.00
• Publications: 10 publications found

Genes affected

LINC02090 (HGNC:52941): (long intergenic non-protein coding RNA 2090)

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (REVEL=0.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.493 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02090	NR_146886.1	n.232G>A		non_coding_transcript_exon_variant	Exon 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02090	ENST00000419151.2	n.232G>A		non_coding_transcript_exon_variant	Exon 2 of 3	3
LINC02090	ENST00000841732.1	n.108G>A		non_coding_transcript_exon_variant	Exon 2 of 4
LINC02090	ENST00000841734.1	n.87G>A		non_coding_transcript_exon_variant	Exon 2 of 3

Frequencies

GnomAD3 genomes AF: 0.382 AC: 58045 AN: 151968 Hom.: 11602 Cov.: 32

Gnomad AFR AF: 0.498

Gnomad AMI AF: 0.171

Gnomad AMR AF: 0.350

Gnomad ASJ AF: 0.373

Gnomad EAS AF: 0.261

Gnomad SAS AF: 0.451

Gnomad FIN AF: 0.363

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.329

Gnomad OTH AF: 0.380

GnomAD2 exomes AF: 0.349 AC: 52248 AN: 149604 AF XY: 0.354

Gnomad AFR exome AF: 0.507

Gnomad AMR exome AF: 0.291

Gnomad ASJ exome AF: 0.360

Gnomad EAS exome AF: 0.240

Gnomad FIN exome AF: 0.359

Gnomad NFE exome AF: 0.333

Gnomad OTH exome AF: 0.352

GnomAD4 exome AF: 0.355 AC: 113318 AN: 318942 Hom.: 20729 Cov.: 0 AF XY: 0.361 AC XY: 65017 AN XY: 180174

African (AFR) AF: 0.507 AC: 4380 AN: 8632

American (AMR) AF: 0.290 AC: 7910 AN: 27280

Ashkenazi Jewish (ASJ) AF: 0.362 AC: 3904 AN: 10790

East Asian (EAS) AF: 0.250 AC: 2305 AN: 9214

South Asian (SAS) AF: 0.437 AC: 26106 AN: 59740

European-Finnish (FIN) AF: 0.361 AC: 9798 AN: 27110

Middle Eastern (MID) AF: 0.364 AC: 1012 AN: 2784

European-Non Finnish (NFE) AF: 0.331 AC: 52704 AN: 159030

Other (OTH) AF: 0.362 AC: 5199 AN: 14362

GnomAD4 genome AF: 0.383 AC: 58174 AN: 152086 Hom.: 11658 Cov.: 32 AF XY: 0.381 AC XY: 28333 AN XY: 74364

African (AFR) AF: 0.499 AC: 20689 AN: 41456

American (AMR) AF: 0.350 AC: 5344 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.373 AC: 1293 AN: 3470

East Asian (EAS) AF: 0.261 AC: 1349 AN: 5170

South Asian (SAS) AF: 0.452 AC: 2180 AN: 4824

European-Finnish (FIN) AF: 0.363 AC: 3840 AN: 10574

Middle Eastern (MID) AF: 0.361 AC: 106 AN: 294

European-Non Finnish (NFE) AF: 0.329 AC: 22399 AN: 67996

Other (OTH) AF: 0.387 AC: 818 AN: 2114

Alfa AF: 0.345 Hom.: 20617

Bravo AF: 0.380

Asia WGS AF: 0.427 AC: 1486 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	0.28
DANN	Benign	0.44
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs9907308; hg19: chr17-16892265;