14-82746900-C-T

Variant names:

• chr14-82746900-C-T
• rs1242553
• ENST00000662642.1:n.*236C>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000662642.1(LINC02301):​n.*236C>T variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.851 in 150,842 control chromosomes in the GnomAD database, including 55,741 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 0.85 (55741 hom., cov: 26)
• Consequence: LINC02301 ENST00000662642.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.176

Genes affected

LINC02301 (HGNC:53220): (long intergenic non-protein coding RNA 2301)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.939 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
LINC02301	ENST00000662642.1	n.*236C>T		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.851 AC: 128329 AN: 150726 Hom.: 55708 Cov.: 26

Gnomad AFR AF: 0.679

Gnomad AMI AF: 0.985

Gnomad AMR AF: 0.890

Gnomad ASJ AF: 0.959

Gnomad EAS AF: 0.675

Gnomad SAS AF: 0.814

Gnomad FIN AF: 0.907

Gnomad MID AF: 0.911

Gnomad NFE AF: 0.945

Gnomad OTH AF: 0.864

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

GnomAD4 genome AF: 0.851 AC: 128412 AN: 150842 Hom.: 55741 Cov.: 26 AF XY: 0.850 AC XY: 62544 AN XY: 73610

Gnomad4 AFR AF: 0.679

Gnomad4 AMR AF: 0.890

Gnomad4 ASJ AF: 0.959

Gnomad4 EAS AF: 0.675

Gnomad4 SAS AF: 0.814

Gnomad4 FIN AF: 0.907

Gnomad4 NFE AF: 0.945

Gnomad4 OTH AF: 0.864

Alfa AF: 0.903 Hom.: 7347

Bravo AF: 0.841

Asia WGS AF: 0.746 AC: 2594 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.4
DANN	Benign	0.94

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1242553; hg19: chr14-83213244;