14-57140349-T-C

Variant names:

• chr14-57140349-T-C
• rs7144018
• ENST00000554725.1:n.345-1645T>C

Variant summary

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

The ENST00000554725.1(OTX2-AS1):​n.345-1645T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.278 in 152,236 control chromosomes in the GnomAD database, including 11,977 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 0.28 (11977 hom., cov: 32)
• Consequence: OTX2-AS1 ENST00000554725.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.93
• Publications: 15 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.725 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.345-1645T>C		intron_variant	Intron 2 of 3	3

Frequencies

GnomAD3 genomes AF: 0.278 AC: 42244 AN: 152118 Hom.: 11933 Cov.: 32

Gnomad AFR AF: 0.732

Gnomad AMI AF: 0.0351

Gnomad AMR AF: 0.162

Gnomad ASJ AF: 0.0752

Gnomad EAS AF: 0.0698

Gnomad SAS AF: 0.0925

Gnomad FIN AF: 0.0677

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.105

Gnomad OTH AF: 0.234

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

GnomAD4 genome AF: 0.278 AC: 42349 AN: 152236 Hom.: 11977 Cov.: 32 AF XY: 0.269 AC XY: 20029 AN XY: 74440

African (AFR) AF: 0.732 AC: 30378 AN: 41492

American (AMR) AF: 0.162 AC: 2474 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0752 AC: 261 AN: 3472

East Asian (EAS) AF: 0.0696 AC: 361 AN: 5188

South Asian (SAS) AF: 0.0932 AC: 450 AN: 4826

European-Finnish (FIN) AF: 0.0677 AC: 718 AN: 10610

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.105 AC: 7131 AN: 68024

Other (OTH) AF: 0.235 AC: 497 AN: 2116

Alfa AF: 0.142 Hom.: 9430

Bravo AF: 0.303

Asia WGS AF: 0.120 AC: 418 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.0060
DANN	Benign	0.36
PhyloP100		-3.9

Splicing

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

Other links and lift over

dbSNP: rs7144018; hg19: chr14-57607067;