chr14-28554895-C-T

Variant names:

• chr14-28554895-C-T
• rs11621151
• ENST00000757289.1:n.384+5366G>A

Variant summary

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

The ENST00000757289.1(LINC02300):​n.384+5366G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0815 in 152,062 control chromosomes in the GnomAD database, including 744 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 0.082 (744 hom., cov: 32)
• Consequence: LINC02300 ENST00000757289.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.307
• 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.204 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.384+5366G>A		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.0814 AC: 12363 AN: 151942 Hom.: 735 Cov.: 32

Gnomad AFR AF: 0.0470

Gnomad AMI AF: 0.124

Gnomad AMR AF: 0.208

Gnomad ASJ AF: 0.129

Gnomad EAS AF: 0.0313

Gnomad SAS AF: 0.0408

Gnomad FIN AF: 0.0721

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0791

Gnomad OTH AF: 0.0761

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

GnomAD4 genome AF: 0.0815 AC: 12396 AN: 152062 Hom.: 744 Cov.: 32 AF XY: 0.0824 AC XY: 6125 AN XY: 74324

African (AFR) AF: 0.0470 AC: 1950 AN: 41516

American (AMR) AF: 0.210 AC: 3196 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.129 AC: 446 AN: 3468

East Asian (EAS) AF: 0.0314 AC: 162 AN: 5166

South Asian (SAS) AF: 0.0414 AC: 200 AN: 4826

European-Finnish (FIN) AF: 0.0721 AC: 763 AN: 10588

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.0791 AC: 5377 AN: 67936

Other (OTH) AF: 0.0753 AC: 159 AN: 2112

Alfa AF: 0.0852 Hom.: 1223

Bravo AF: 0.0896

Asia WGS AF: 0.0460 AC: 160 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	8.5
DANN	Benign	0.49
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs11621151; hg19: chr14-29024101;