14-25841023-G-A

Position:

• chr14-25841023-G-A

Variant summary

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

The ENST00000546412.2(LINC02306):​n.259-2493C>T 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 0.443 in 151,710 control chromosomes in the GnomAD database, including 17,844 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 0.44 (17844 hom., cov: 31)
• Consequence: LINC02306 ENST00000546412.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.831

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=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.588 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02306	ENST00000546412.2	n.259-2493C>T		intron_variant, non_coding_transcript_variant		3
LINC02306	ENST00000657312.1	n.459-2493C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.443 AC: 67167 AN: 151592 Hom.: 17854 Cov.: 31

Gnomad AFR AF: 0.142

Gnomad AMI AF: 0.772

Gnomad AMR AF: 0.514

Gnomad ASJ AF: 0.618

Gnomad EAS AF: 0.363

Gnomad SAS AF: 0.315

Gnomad FIN AF: 0.549

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.593

Gnomad OTH AF: 0.487

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

GnomAD4 genome AF: 0.443 AC: 67155 AN: 151710 Hom.: 17844 Cov.: 31 AF XY: 0.439 AC XY: 32563 AN XY: 74094

Gnomad4 AFR AF: 0.142

Gnomad4 AMR AF: 0.514

Gnomad4 ASJ AF: 0.618

Gnomad4 EAS AF: 0.363

Gnomad4 SAS AF: 0.315

Gnomad4 FIN AF: 0.549

Gnomad4 NFE AF: 0.593

Gnomad4 OTH AF: 0.484

Alfa AF: 0.504 Hom.: 2878

Bravo AF: 0.430

Asia WGS AF: 0.308 AC: 1072 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.30
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2105274; hg19: chr14-26310229;