rs2296091

Variant names:

• chr14-56952667-C-T
• rs2296091
• ENST00000554725.1:n.344+1146C>T

Variant summary

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

The ENST00000554725.1(OTX2-AS1):​n.344+1146C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.213 in 151,442 control chromosomes in the GnomAD database, including 3,988 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 0.21 (3988 hom., cov: 31)
• Consequence: OTX2-AS1 ENST00000554725.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.423

Genes affected

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

ENSG00000286257 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.275 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
OTX2-AS1	ENST00000554725.1	n.344+1146C>T		intron_variant	Intron 2 of 3	3
ENSG00000286257	ENST00000651959.1	n.714-1060G>A		intron_variant	Intron 2 of 2
ENSG00000286257	ENST00000669623.1	n.581-1060G>A		intron_variant	Intron 3 of 3
ENSG00000286257	ENST00000669773.1	n.571-1060G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.214 AC: 32318 AN: 151348 Hom.: 3990 Cov.: 31

Gnomad AFR AF: 0.105

Gnomad AMI AF: 0.148

Gnomad AMR AF: 0.224

Gnomad ASJ AF: 0.263

Gnomad EAS AF: 0.0678

Gnomad SAS AF: 0.147

Gnomad FIN AF: 0.293

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.279

Gnomad OTH AF: 0.221

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

GnomAD4 genome AF: 0.213 AC: 32304 AN: 151442 Hom.: 3988 Cov.: 31 AF XY: 0.213 AC XY: 15740 AN XY: 73918

Gnomad4 AFR AF: 0.105

Gnomad4 AMR AF: 0.224

Gnomad4 ASJ AF: 0.263

Gnomad4 EAS AF: 0.0672

Gnomad4 SAS AF: 0.147

Gnomad4 FIN AF: 0.293

Gnomad4 NFE AF: 0.279

Gnomad4 OTH AF: 0.219

Alfa AF: 0.255 Hom.: 2511

Bravo AF: 0.204

Asia WGS AF: 0.120 AC: 416 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.7
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2296091; hg19: chr14-57419385;