14-28984835-A-G

Variant names:

• chr14-28984835-A-G
• rs12587874
• ENST00000551227.1:n.108-1565A>G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000552028.2(LINC02326):​n.462-5817T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.149 in 152,162 control chromosomes in the GnomAD database, including 2,268 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 0.15 (2268 hom., cov: 32)
• Consequence: LINC02326 ENST00000552028.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.63
• Publications: 1 publications found

Genes affected

LINC02327 (HGNC:53247): (long intergenic non-protein coding RNA 2327)

LINC02326 (HGNC:53246): (long intergenic non-protein coding RNA 2326)

ENSG00000257522 (HGNC:58970):

LOC107984685 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.45).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.462 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000552028.2. 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
	LINC02326	NR_184205.1		n.338-5817T>C		intron	N/A
	LINC02326	NR_184206.1		n.237-5817T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02327	ENST00000551227.1	TSL:5	n.108-1565A>G		intron	N/A
	LINC02326	ENST00000552028.2	TSL:3	n.462-5817T>C		intron	N/A
	LINC02326	ENST00000650159.1		n.292+44605T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.149 AC: 22628 AN: 152042 Hom.: 2268 Cov.: 32

Gnomad AFR AF: 0.0506

Gnomad AMI AF: 0.0976

Gnomad AMR AF: 0.163

Gnomad ASJ AF: 0.166

Gnomad EAS AF: 0.479

Gnomad SAS AF: 0.259

Gnomad FIN AF: 0.176

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.168

Gnomad OTH AF: 0.155

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

GnomAD4 genome AF: 0.149 AC: 22638 AN: 152162 Hom.: 2268 Cov.: 32 AF XY: 0.155 AC XY: 11500 AN XY: 74382

African (AFR) AF: 0.0506 AC: 2103 AN: 41578

American (AMR) AF: 0.163 AC: 2487 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.166 AC: 577 AN: 3468

East Asian (EAS) AF: 0.478 AC: 2466 AN: 5158

South Asian (SAS) AF: 0.259 AC: 1249 AN: 4816

European-Finnish (FIN) AF: 0.176 AC: 1863 AN: 10596

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.168 AC: 11414 AN: 67962

Other (OTH) AF: 0.159 AC: 336 AN: 2112

Alfa AF: 0.146 Hom.: 302

Bravo AF: 0.145

Asia WGS AF: 0.342 AC: 1182 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.45
CADD	Benign	13
DANN	Benign	0.87
PhyloP100		1.6

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: rs12587874;

hg19: chr14-29454041;