chr14-25660360-G-T

Position:

• chr14-25660360-G-T

Variant summary

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

The ENST00000546412.2(LINC02306):​n.928+486C>A 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 0.0429 in 152,158 control chromosomes in the GnomAD database, including 763 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 0.043 (763 hom., cov: 32)
• Consequence: LINC02306 ENST00000546412.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0510

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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.473 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.928+486C>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.0429 AC: 6520 AN: 152040 Hom.: 761 Cov.: 32

Gnomad AFR AF: 0.00881

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0474

Gnomad ASJ AF: 0.0297

Gnomad EAS AF: 0.488

Gnomad SAS AF: 0.159

Gnomad FIN AF: 0.0405

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0224

Gnomad OTH AF: 0.0441

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

GnomAD4 genome AF: 0.0429 AC: 6521 AN: 152158 Hom.: 763 Cov.: 32 AF XY: 0.0478 AC XY: 3558 AN XY: 74382

Gnomad4 AFR AF: 0.00879

Gnomad4 AMR AF: 0.0471

Gnomad4 ASJ AF: 0.0297

Gnomad4 EAS AF: 0.489

Gnomad4 SAS AF: 0.160

Gnomad4 FIN AF: 0.0405

Gnomad4 NFE AF: 0.0224

Gnomad4 OTH AF: 0.0446

Alfa AF: 0.0359 Hom.: 103

Bravo AF: 0.0422

Asia WGS AF: 0.253 AC: 880 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.3
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12586774; hg19: chr14-26129566;