chr14-86382114-A-G

Position:

• chr14-86382114-A-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000553679.1(LINC02309):​n.134-19098A>G variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.643

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02309	ENST00000553679.1	n.134-19098A>G		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.278

Gnomad4 AMR AF: 0.470

Gnomad4 ASJ AF: 0.514

Gnomad4 EAS AF: 0.288

Gnomad4 SAS AF: 0.495

Gnomad4 FIN AF: 0.509

Gnomad4 NFE AF: 0.461

Gnomad4 OTH AF: 0.433

Alfa AF: 0.430 Hom.: 6945

Bravo AF: 0.397

Asia WGS AF: 0.340 AC: 1185 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs804963; hg19: chr14-86848458;