ENST00000757289.1:n.342-16203T>G

Variant names:

• chr14-28576506-A-C
• rs10130803
• ENST00000757289.1:n.342-16203T>G

Variant summary

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

The ENST00000757289.1(LINC02300):​n.342-16203T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.859 in 152,142 control chromosomes in the GnomAD database, including 56,115 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 0.86 (56115 hom., cov: 33)
• Consequence: LINC02300 ENST00000757289.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.841
• Publications: 1 publications found

Genes affected

LINC02300 (HGNC:53219): (long intergenic non-protein coding RNA 2300)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.87 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
LINC02300	ENST00000757289.1	n.342-16203T>G		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.859 AC: 130511 AN: 152022 Hom.: 56063 Cov.: 33

Gnomad AFR AF: 0.853

Gnomad AMI AF: 0.897

Gnomad AMR AF: 0.882

Gnomad ASJ AF: 0.874

Gnomad EAS AF: 0.886

Gnomad SAS AF: 0.802

Gnomad FIN AF: 0.888

Gnomad MID AF: 0.850

Gnomad NFE AF: 0.853

Gnomad OTH AF: 0.859

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

GnomAD4 genome AF: 0.859 AC: 130624 AN: 152142 Hom.: 56115 Cov.: 33 AF XY: 0.859 AC XY: 63888 AN XY: 74376

African (AFR) AF: 0.853 AC: 35389 AN: 41488

American (AMR) AF: 0.882 AC: 13484 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.874 AC: 3033 AN: 3470

East Asian (EAS) AF: 0.886 AC: 4575 AN: 5166

South Asian (SAS) AF: 0.803 AC: 3871 AN: 4820

European-Finnish (FIN) AF: 0.888 AC: 9414 AN: 10606

Middle Eastern (MID) AF: 0.840 AC: 247 AN: 294

European-Non Finnish (NFE) AF: 0.853 AC: 57979 AN: 67996

Other (OTH) AF: 0.861 AC: 1816 AN: 2110

Alfa AF: 0.852 Hom.: 8313

Bravo AF: 0.860

Asia WGS AF: 0.834 AC: 2901 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	4.5
DANN	Benign	0.76
PhyloP100		-0.84

Splicing

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

Other links and lift over

dbSNP: rs10130803; hg19: chr14-29045712;