14-26008955-T-C

Variant names:

• chr14-26008955-T-C
• rs862966
• ENST00000546412.2:n.258+117202A>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000546412.2(LINC02306):​n.258+117202A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.379 in 152,070 control chromosomes in the GnomAD database, including 11,469 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 0.38 (11469 hom., cov: 32)
• Consequence: LINC02306 ENST00000546412.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0170

Genes affected

LINC02306 (HGNC:53225): (long intergenic non-protein coding RNA 2306)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.443 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02306	ENST00000546412.2	n.258+117202A>G		intron_variant	Intron 2 of 9	3
LINC02306	ENST00000657312.1	n.458+117202A>G		intron_variant	Intron 3 of 6

Frequencies

GnomAD3 genomes AF: 0.379 AC: 57557 AN: 151950 Hom.: 11467 Cov.: 32

Gnomad AFR AF: 0.256

Gnomad AMI AF: 0.651

Gnomad AMR AF: 0.343

Gnomad ASJ AF: 0.431

Gnomad EAS AF: 0.426

Gnomad SAS AF: 0.388

Gnomad FIN AF: 0.403

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.447

Gnomad OTH AF: 0.387

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

GnomAD4 genome AF: 0.379 AC: 57586 AN: 152070 Hom.: 11469 Cov.: 32 AF XY: 0.377 AC XY: 28055 AN XY: 74334

Gnomad4 AFR AF: 0.256

Gnomad4 AMR AF: 0.343

Gnomad4 ASJ AF: 0.431

Gnomad4 EAS AF: 0.427

Gnomad4 SAS AF: 0.389

Gnomad4 FIN AF: 0.403

Gnomad4 NFE AF: 0.447

Gnomad4 OTH AF: 0.387

Alfa AF: 0.433 Hom.: 19209

Bravo AF: 0.369

Asia WGS AF: 0.424 AC: 1475 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.5
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs862966; hg19: chr14-26478161;