14-28537548-A-G

Variant names:

• chr14-28537548-A-G
• rs10141935
• ENST00000757289.1:n.384+22713T>C

Variant summary

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

The ENST00000757289.1(LINC02300):​n.384+22713T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.369 in 151,816 control chromosomes in the GnomAD database, including 10,631 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 0.37 (10631 hom., cov: 31)
• Consequence: LINC02300 ENST00000757289.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.330
• Publications: 5 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=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.423 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000757289.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02300	ENST00000757289.1		n.384+22713T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.369 AC: 56001 AN: 151696 Hom.: 10626 Cov.: 31

Gnomad AFR AF: 0.312

Gnomad AMI AF: 0.392

Gnomad AMR AF: 0.356

Gnomad ASJ AF: 0.366

Gnomad EAS AF: 0.135

Gnomad SAS AF: 0.255

Gnomad FIN AF: 0.396

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.427

Gnomad OTH AF: 0.401

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

GnomAD4 genome AF: 0.369 AC: 56030 AN: 151816 Hom.: 10631 Cov.: 31 AF XY: 0.365 AC XY: 27078 AN XY: 74162

African (AFR) AF: 0.311 AC: 12891 AN: 41396

American (AMR) AF: 0.356 AC: 5432 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.366 AC: 1270 AN: 3468

East Asian (EAS) AF: 0.135 AC: 696 AN: 5166

South Asian (SAS) AF: 0.255 AC: 1225 AN: 4804

European-Finnish (FIN) AF: 0.396 AC: 4155 AN: 10496

Middle Eastern (MID) AF: 0.442 AC: 130 AN: 294

European-Non Finnish (NFE) AF: 0.427 AC: 29024 AN: 67906

Other (OTH) AF: 0.403 AC: 850 AN: 2110

Alfa AF: 0.407 Hom.: 55246

Bravo AF: 0.365

Asia WGS AF: 0.243 AC: 845 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	10
DANN	Benign	0.84
PhyloP100		0.33

Splicing

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

Other links and lift over

dbSNP: rs10141935; hg19: chr14-29006754;