rs999881

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr14-57061918-C-G
• chr14-57061918-C-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000554725.1(OTX2-AS1):​n.345-80076C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.548 in 151,946 control chromosomes in the GnomAD database, including 23,529 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 0.55 (23529 hom., 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.682 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.345-80076C>G		intron_variant	Intron 2 of 3	3
LINC03059	ENST00000716872.1	n.126+50277G>C		intron_variant	Intron 1 of 1
LINC03059	ENST00000716873.1	n.491-46372G>C		intron_variant	Intron 1 of 2
LINC03059	ENST00000716874.1	n.480-28068G>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.548 AC: 83200 AN: 151828 Hom.: 23505 Cov.: 32

Gnomad AFR AF: 0.689

Gnomad AMI AF: 0.396

Gnomad AMR AF: 0.480

Gnomad ASJ AF: 0.470

Gnomad EAS AF: 0.621

Gnomad SAS AF: 0.494

Gnomad FIN AF: 0.491

Gnomad MID AF: 0.452

Gnomad NFE AF: 0.492

Gnomad OTH AF: 0.529

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

GnomAD4 genome AF: 0.548 AC: 83280 AN: 151946 Hom.: 23529 Cov.: 32 AF XY: 0.545 AC XY: 40507 AN XY: 74274

African (AFR) AF: 0.689 AC: 28523 AN: 41398

American (AMR) AF: 0.480 AC: 7339 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.470 AC: 1631 AN: 3472

East Asian (EAS) AF: 0.620 AC: 3193 AN: 5152

South Asian (SAS) AF: 0.494 AC: 2377 AN: 4812

European-Finnish (FIN) AF: 0.491 AC: 5188 AN: 10566

Middle Eastern (MID) AF: 0.469 AC: 137 AN: 292

European-Non Finnish (NFE) AF: 0.492 AC: 33417 AN: 67958

Other (OTH) AF: 0.531 AC: 1115 AN: 2100

Alfa AF: 0.520 Hom.: 2607

Bravo AF: 0.553

Asia WGS AF: 0.544 AC: 1892 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.3
DANN	Benign	0.63
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;