chr14-56971771-G-A

Variant names:

• chr14-56971771-G-A
• rs6573113
• ENST00000554725.1:n.344+20250G>A

Variant summary

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

The ENST00000554725.1(OTX2-AS1):​n.344+20250G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.232 in 151,984 control chromosomes in the GnomAD database, including 5,123 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 0.23 (5123 hom., cov: 32)
• Consequence: OTX2-AS1 ENST00000554725.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.804
• Publications: 2 publications found

Genes affected

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

ENSG00000286257 (HGNC:):

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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.407 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000554725.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OTX2-AS1	ENST00000554725.1	TSL:3	n.344+20250G>A		intron	N/A
	ENSG00000286257	ENST00000651959.1		n.441-17187C>T		intron	N/A
	ENSG00000286257	ENST00000653538.1		n.1162-17187C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.232 AC: 35165 AN: 151866 Hom.: 5113 Cov.: 32

Gnomad AFR AF: 0.412

Gnomad AMI AF: 0.152

Gnomad AMR AF: 0.162

Gnomad ASJ AF: 0.126

Gnomad EAS AF: 0.0437

Gnomad SAS AF: 0.166

Gnomad FIN AF: 0.152

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.177

Gnomad OTH AF: 0.205

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

GnomAD4 genome AF: 0.232 AC: 35202 AN: 151984 Hom.: 5123 Cov.: 32 AF XY: 0.227 AC XY: 16880 AN XY: 74312

African (AFR) AF: 0.412 AC: 17056 AN: 41416

American (AMR) AF: 0.161 AC: 2461 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.126 AC: 437 AN: 3470

East Asian (EAS) AF: 0.0438 AC: 227 AN: 5178

South Asian (SAS) AF: 0.167 AC: 805 AN: 4818

European-Finnish (FIN) AF: 0.152 AC: 1605 AN: 10554

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.177 AC: 12003 AN: 67960

Other (OTH) AF: 0.203 AC: 429 AN: 2110

Alfa AF: 0.184 Hom.: 3608

Bravo AF: 0.239

Asia WGS AF: 0.126 AC: 437 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.3
DANN	Benign	0.41
PhyloP100		0.80

Splicing

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

Other links and lift over

dbSNP: rs6573113; hg19: chr14-57438489;