chr14-82704378-A-T

Variant names:

• chr14-82704378-A-T
• rs2150333
• ENST00000555150.6:n.316-2323A>T

Variant summary

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

The ENST00000555150.6(LINC02301):​n.316-2323A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.113 in 152,038 control chromosomes in the GnomAD database, including 1,255 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 0.11 (1255 hom., cov: 32)
• Consequence: LINC02301 ENST00000555150.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.337
• Publications: 2 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.344 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000555150.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02301	NR_146650.1		n.304-2323A>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02301	ENST00000555150.6	TSL:3	n.316-2323A>T		intron	N/A
	LINC02301	ENST00000662642.1		n.184+17009A>T		intron	N/A
	LINC02301	ENST00000841947.1		n.182+17009A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.113 AC: 17149 AN: 151920 Hom.: 1253 Cov.: 32

Gnomad AFR AF: 0.140

Gnomad AMI AF: 0.130

Gnomad AMR AF: 0.139

Gnomad ASJ AF: 0.0524

Gnomad EAS AF: 0.358

Gnomad SAS AF: 0.194

Gnomad FIN AF: 0.0854

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0736

Gnomad OTH AF: 0.116

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

GnomAD4 genome AF: 0.113 AC: 17161 AN: 152038 Hom.: 1255 Cov.: 32 AF XY: 0.118 AC XY: 8750 AN XY: 74288

African (AFR) AF: 0.140 AC: 5805 AN: 41460

American (AMR) AF: 0.139 AC: 2123 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.0524 AC: 182 AN: 3470

East Asian (EAS) AF: 0.358 AC: 1840 AN: 5142

South Asian (SAS) AF: 0.193 AC: 930 AN: 4816

European-Finnish (FIN) AF: 0.0854 AC: 903 AN: 10576

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0736 AC: 5004 AN: 67992

Other (OTH) AF: 0.114 AC: 242 AN: 2116

Alfa AF: 0.0886 Hom.: 89

Bravo AF: 0.118

Asia WGS AF: 0.279 AC: 969 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.6
DANN	Benign	0.55
PhyloP100		0.34

Splicing

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

Other links and lift over

dbSNP: rs2150333; hg19: chr14-83170722;