14-82745081-T-C

Variant names:

• chr14-82745081-T-C
• rs1242550
• ENST00000662642.1:n.323-301T>C

Variant summary

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

The ENST00000662642.1(LINC02301):​n.323-301T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.83 in 152,070 control chromosomes in the GnomAD database, including 53,222 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 0.83 (53222 hom., cov: 31)
• Consequence: LINC02301 ENST00000662642.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.277

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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.91 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.323-301T>C		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.830 AC: 126063 AN: 151952 Hom.: 53187 Cov.: 31

Gnomad AFR AF: 0.675

Gnomad AMI AF: 0.939

Gnomad AMR AF: 0.869

Gnomad ASJ AF: 0.882

Gnomad EAS AF: 0.677

Gnomad SAS AF: 0.807

Gnomad FIN AF: 0.881

Gnomad MID AF: 0.861

Gnomad NFE AF: 0.916

Gnomad OTH AF: 0.840

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

GnomAD4 genome AF: 0.830 AC: 126150 AN: 152070 Hom.: 53222 Cov.: 31 AF XY: 0.829 AC XY: 61622 AN XY: 74326

Gnomad4 AFR AF: 0.675

Gnomad4 AMR AF: 0.869

Gnomad4 ASJ AF: 0.882

Gnomad4 EAS AF: 0.678

Gnomad4 SAS AF: 0.807

Gnomad4 FIN AF: 0.881

Gnomad4 NFE AF: 0.916

Gnomad4 OTH AF: 0.840

Alfa AF: 0.871 Hom.: 7236

Bravo AF: 0.820

Asia WGS AF: 0.745 AC: 2594 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.5
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1242550; hg19: chr14-83211425;