rs9907308

chr17-16988951-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_146886.1(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 NR_146886.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.00

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• 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/exons	MANE	UniProt
LINC02090	NR_146886.1	n.232G>A		non_coding_transcript_exon_variant	2/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02090	ENST00000419151.2	n.232G>A		non_coding_transcript_exon_variant	2/3	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

GnomAD3 exomes AF: 0.349 AC: 52248 AN: 149604 Hom.: 9509 AF XY: 0.354 AC XY: 28470 AN XY: 80476

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 SAS exome AF: 0.445

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

Gnomad4 AFR exome AF: 0.507

Gnomad4 AMR exome AF: 0.290

Gnomad4 ASJ exome AF: 0.362

Gnomad4 EAS exome AF: 0.250

Gnomad4 SAS exome AF: 0.437

Gnomad4 FIN exome AF: 0.361

Gnomad4 NFE exome AF: 0.331

Gnomad4 OTH exome AF: 0.362

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

Gnomad4 AFR AF: 0.499

Gnomad4 AMR AF: 0.350

Gnomad4 ASJ AF: 0.373

Gnomad4 EAS AF: 0.261

Gnomad4 SAS AF: 0.452

Gnomad4 FIN AF: 0.363

Gnomad4 NFE AF: 0.329

Gnomad4 OTH AF: 0.387

Alfa AF: 0.340 Hom.: 15397

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9907308; hg19: chr17-16892265;