rs2296091

chr14-56952667-C-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, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.423

Genes affected

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

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
OTX2-AS1	ENST00000554725.1	n.344+1146C>T		intron_variant, non_coding_transcript_variant		3
	ENST00000651959.1	n.714-1060G>A		intron_variant, non_coding_transcript_variant
	ENST00000669623.1	n.581-1060G>A		intron_variant, non_coding_transcript_variant
	ENST00000669773.1	n.571-1060G>A		intron_variant, non_coding_transcript_variant

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;