rs1189827

Variant names:

• chr14-57066746-G-A
• rs1189827
• ENST00000554160.1:n.625C>T

Variant summary

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

The ENST00000554160.1(LINC03059):​n.625C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.579 in 151,948 control chromosomes in the GnomAD database, including 26,072 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 0.58 (26072 hom., cov: 32)
  • Exomes 𝑓: 0.25 (0 hom.)
• Consequence: LINC03059 ENST00000554160.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.269
• Publications: 2 publications found

Genes affected

LINC03059 (HGNC:56366): (long intergenic non-protein coding RNA 3059)

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.695 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
LINC03059	ENST00000554160.1	n.625C>T		non_coding_transcript_exon_variant	Exon 3 of 3	2
LINC03059	ENST00000716875.1	n.1092C>T		non_coding_transcript_exon_variant	Exon 3 of 3
LINC03059	ENST00000716878.1	n.549C>T		non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.579 AC: 87941 AN: 151824 Hom.: 26030 Cov.: 32

Gnomad AFR AF: 0.701

Gnomad AMI AF: 0.425

Gnomad AMR AF: 0.516

Gnomad ASJ AF: 0.552

Gnomad EAS AF: 0.591

Gnomad SAS AF: 0.487

Gnomad FIN AF: 0.490

Gnomad MID AF: 0.571

Gnomad NFE AF: 0.542

Gnomad OTH AF: 0.577

GnomAD4 exome AF: 0.250 AC: 1 AN: 4 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.500 AC: 1 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AF: 0.00 AC: 0 AN: 2

GnomAD4 genome AF: 0.579 AC: 88049 AN: 151944 Hom.: 26072 Cov.: 32 AF XY: 0.573 AC XY: 42556 AN XY: 74270

African (AFR) AF: 0.702 AC: 29083 AN: 41446

American (AMR) AF: 0.516 AC: 7878 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.552 AC: 1914 AN: 3470

East Asian (EAS) AF: 0.590 AC: 3036 AN: 5148

South Asian (SAS) AF: 0.487 AC: 2346 AN: 4816

European-Finnish (FIN) AF: 0.490 AC: 5157 AN: 10532

Middle Eastern (MID) AF: 0.579 AC: 169 AN: 292

European-Non Finnish (NFE) AF: 0.542 AC: 36854 AN: 67940

Other (OTH) AF: 0.579 AC: 1225 AN: 2116

Alfa AF: 0.555 Hom.: 74714

Bravo AF: 0.587

Asia WGS AF: 0.542 AC: 1884 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.19
DANN	Benign	0.68
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs1189827; hg19: chr14-57533464;