ENST00000553668.2:n.183-990A>G

Variant names:

• chr14-86126960-A-G
• rs10498602
• ENST00000553668.2:n.183-990A>G

Variant summary

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

The ENST00000553668.2(LINC02328):​n.183-990A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0221 in 152,180 control chromosomes in the GnomAD database, including 123 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 0.022 (123 hom., cov: 32)
• Consequence: LINC02328 ENST00000553668.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0690
• Publications: 0 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.11 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.290-990A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02328	ENST00000553668.2	TSL:3	n.183-990A>G		intron	N/A
	LINC02328	ENST00000557195.5	TSL:3	n.446-990A>G		intron	N/A
	LINC02328	ENST00000654590.3		n.395-990A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0220 AC: 3340 AN: 152062 Hom.: 122 Cov.: 32

Gnomad AFR AF: 0.00618

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0752

Gnomad ASJ AF: 0.00202

Gnomad EAS AF: 0.117

Gnomad SAS AF: 0.0414

Gnomad FIN AF: 0.0354

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0105

Gnomad OTH AF: 0.0153

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

GnomAD4 genome AF: 0.0221 AC: 3358 AN: 152180 Hom.: 123 Cov.: 32 AF XY: 0.0249 AC XY: 1852 AN XY: 74408

African (AFR) AF: 0.00621 AC: 258 AN: 41564

American (AMR) AF: 0.0754 AC: 1152 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.00202 AC: 7 AN: 3468

East Asian (EAS) AF: 0.118 AC: 609 AN: 5182

South Asian (SAS) AF: 0.0414 AC: 200 AN: 4828

European-Finnish (FIN) AF: 0.0354 AC: 375 AN: 10602

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.0105 AC: 711 AN: 67942

Other (OTH) AF: 0.0204 AC: 43 AN: 2112

Alfa AF: 0.0156 Hom.: 7

Bravo AF: 0.0254

Asia WGS AF: 0.0870 AC: 302 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.69
DANN	Benign	0.39
PhyloP100		-0.069

Splicing

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

Other links and lift over

dbSNP: rs10498602; hg19: chr14-86593304;