ENST00000554725.1:n.345-80076C>T

Variant names:

• chr14-57061918-C-T
• rs999881
• ENST00000554725.1:n.345-80076C>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000554725.1(OTX2-AS1):​n.345-80076C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• Consequence: OTX2-AS1 ENST00000554725.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.186
• Publications: 4 publications found

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

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).

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.345-80076C>T		intron_variant	Intron 2 of 3	3
LINC03059	ENST00000716872.1	n.126+50277G>A		intron_variant	Intron 1 of 1
LINC03059	ENST00000716873.1	n.491-46372G>A		intron_variant	Intron 1 of 2
LINC03059	ENST00000716874.1	n.480-28068G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.9
DANN	Benign	0.92
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs999881; hg19: chr14-57528636;