rs2224437

Variant names:

• chr14-28521221-C-T
• rs2224437
• ENST00000757289.1:n.385-6941G>A

Variant summary

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

The ENST00000757289.1(LINC02300):​n.385-6941G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.45 in 151,978 control chromosomes in the GnomAD database, including 17,598 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 0.45 (17598 hom., cov: 32)
• Consequence: LINC02300 ENST00000757289.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.957
• Publications: 3 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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.701 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.385-6941G>A		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.450 AC: 68378 AN: 151860 Hom.: 17564 Cov.: 32

Gnomad AFR AF: 0.708

Gnomad AMI AF: 0.469

Gnomad AMR AF: 0.294

Gnomad ASJ AF: 0.397

Gnomad EAS AF: 0.163

Gnomad SAS AF: 0.515

Gnomad FIN AF: 0.331

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.369

Gnomad OTH AF: 0.406

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

GnomAD4 genome AF: 0.450 AC: 68463 AN: 151978 Hom.: 17598 Cov.: 32 AF XY: 0.444 AC XY: 32969 AN XY: 74284

African (AFR) AF: 0.708 AC: 29355 AN: 41466

American (AMR) AF: 0.293 AC: 4475 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.397 AC: 1376 AN: 3470

East Asian (EAS) AF: 0.163 AC: 838 AN: 5150

South Asian (SAS) AF: 0.515 AC: 2481 AN: 4814

European-Finnish (FIN) AF: 0.331 AC: 3496 AN: 10552

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.369 AC: 25062 AN: 67954

Other (OTH) AF: 0.403 AC: 848 AN: 2102

Alfa AF: 0.390 Hom.: 51003

Bravo AF: 0.455

Asia WGS AF: 0.326 AC: 1137 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.71
DANN	Benign	0.72
PhyloP100		-0.96

Splicing

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

Other links and lift over

dbSNP: rs2224437; hg19: chr14-28990427;