14-86005780-C-T

Variant names:

• chr14-86005780-C-T
• rs7492316
• ENST00000553668.2:n.77+21758C>T

Variant summary

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

The ENST00000553668.2(LINC02328):​n.77+21758C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0247 in 151,924 control chromosomes in the GnomAD database, including 156 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 0.025 (156 hom., cov: 32)
• Consequence: LINC02328 ENST00000553668.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.56
• Publications: 1 publications found

Genes affected

LINC02328 (HGNC:53248): (long intergenic non-protein coding RNA 2328)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.121 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000553668.2. 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
	LINC02328	NR_110155.1		n.185-65083C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02328	ENST00000553668.2	TSL:3	n.77+21758C>T		intron	N/A
	LINC02328	ENST00000557195.5	TSL:3	n.245+4827C>T		intron	N/A
	LINC02328	ENST00000654590.3		n.290-65083C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0246 AC: 3727 AN: 151806 Hom.: 155 Cov.: 32

Gnomad AFR AF: 0.0126

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0764

Gnomad ASJ AF: 0.00202

Gnomad EAS AF: 0.129

Gnomad SAS AF: 0.0461

Gnomad FIN AF: 0.0354

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0108

Gnomad OTH AF: 0.0168

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

GnomAD4 genome AF: 0.0247 AC: 3755 AN: 151924 Hom.: 156 Cov.: 32 AF XY: 0.0276 AC XY: 2049 AN XY: 74232

African (AFR) AF: 0.0130 AC: 538 AN: 41490

American (AMR) AF: 0.0766 AC: 1164 AN: 15190

Ashkenazi Jewish (ASJ) AF: 0.00202 AC: 7 AN: 3460

East Asian (EAS) AF: 0.129 AC: 668 AN: 5172

South Asian (SAS) AF: 0.0462 AC: 222 AN: 4808

European-Finnish (FIN) AF: 0.0354 AC: 374 AN: 10562

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.0108 AC: 735 AN: 67936

Other (OTH) AF: 0.0205 AC: 43 AN: 2100

Alfa AF: 0.0180 Hom.: 179

Bravo AF: 0.0284

Asia WGS AF: 0.0970 AC: 335 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.042
DANN	Benign	0.76
PhyloP100		-3.6

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7492316;

hg19: chr14-86472124;