rs1189827

chr14-57066746-G-A

Variant summary

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

The ENST00000554725.1(OTX2-AS1):n.345-75248G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.579 in 151,948 control chromosomes in the GnomAD database, including 26,072 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 0.58 (26072 hom., cov: 32)
  • Exomes 𝑓: 0.25 (0 hom.)
• Consequence: OTX2-AS1 ENST00000554725.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.269

Genes affected

OTX2-AS1 (HGNC:43906): (OTX2 antisense RNA 1 (head to head))

LINC03059 (HGNC:56366): (long intergenic non-protein coding RNA 3059)

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 = 0.695 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
OTX2-AS1	ENST00000554725.1	n.345-75248G>A		intron_variant, non_coding_transcript_variant		3
LINC03059	ENST00000554160.1	n.625C>T		non_coding_transcript_exon_variant	3/3	2

Frequencies

GnomAD3 genomes AF: 0.579 AC: 87941 AN: 151824 Hom.: 26030 Cov.: 32

Gnomad AFR AF: 0.701

Gnomad AMI AF: 0.425

Gnomad AMR AF: 0.516

Gnomad ASJ AF: 0.552

Gnomad EAS AF: 0.591

Gnomad SAS AF: 0.487

Gnomad FIN AF: 0.490

Gnomad MID AF: 0.571

Gnomad NFE AF: 0.542

Gnomad OTH AF: 0.577

GnomAD4 exome AF: 0.250 AC: 1 AN: 4 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

Gnomad4 FIN exome AF: 0.500

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.579 AC: 88049 AN: 151944 Hom.: 26072 Cov.: 32 AF XY: 0.573 AC XY: 42556 AN XY: 74270

Gnomad4 AFR AF: 0.702

Gnomad4 AMR AF: 0.516

Gnomad4 ASJ AF: 0.552

Gnomad4 EAS AF: 0.590

Gnomad4 SAS AF: 0.487

Gnomad4 FIN AF: 0.490

Gnomad4 NFE AF: 0.542

Gnomad4 OTH AF: 0.579

Alfa AF: 0.547 Hom.: 46865

Bravo AF: 0.587

Asia WGS AF: 0.542 AC: 1884 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	0.19
Dann	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1189827; hg19: chr14-57533464;