chr14-86382114-A-G

Variant names:

• chr14-86382114-A-G
• rs804963
• ENST00000553679.1:n.134-19098A>G

Variant summary

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

The ENST00000553679.1(LINC02309):​n.134-19098A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.412 in 151,768 control chromosomes in the GnomAD database, including 13,462 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 0.41 (13462 hom., cov: 31)
• Consequence: LINC02309 ENST00000553679.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.643
• Publications: 3 publications found

Genes affected

LINC02309 (HGNC:53228): (long intergenic non-protein coding RNA 2309)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.4).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.479 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000553679.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02309	ENST00000553679.1	TSL:3	n.134-19098A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.412 AC: 62470 AN: 151650 Hom.: 13461 Cov.: 31

Gnomad AFR AF: 0.278

Gnomad AMI AF: 0.540

Gnomad AMR AF: 0.469

Gnomad ASJ AF: 0.514

Gnomad EAS AF: 0.288

Gnomad SAS AF: 0.494

Gnomad FIN AF: 0.509

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.461

Gnomad OTH AF: 0.438

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

GnomAD4 genome AF: 0.412 AC: 62495 AN: 151768 Hom.: 13462 Cov.: 31 AF XY: 0.418 AC XY: 31007 AN XY: 74174

African (AFR) AF: 0.278 AC: 11504 AN: 41416

American (AMR) AF: 0.470 AC: 7146 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.514 AC: 1782 AN: 3470

East Asian (EAS) AF: 0.288 AC: 1482 AN: 5150

South Asian (SAS) AF: 0.495 AC: 2385 AN: 4814

European-Finnish (FIN) AF: 0.509 AC: 5378 AN: 10560

Middle Eastern (MID) AF: 0.455 AC: 133 AN: 292

European-Non Finnish (NFE) AF: 0.461 AC: 31283 AN: 67834

Other (OTH) AF: 0.433 AC: 911 AN: 2102

Alfa AF: 0.432 Hom.: 7730

Bravo AF: 0.397

Asia WGS AF: 0.340 AC: 1185 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.40
CADD	Benign	12
DANN	Benign	0.73
PhyloP100		-0.64

Splicing

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

Other links and lift over

dbSNP: rs804963; hg19: chr14-86848458;