rs1475010

Positions:

• chr14-25667405-C-A
• chr14-25667405-C-G
• chr14-25667405-C-T

Variant summary

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

The ENST00000546412.2(LINC02306):​n.538-2430G>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 0.465 in 151,798 control chromosomes in the GnomAD database, including 19,402 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 0.47 (19402 hom., cov: 31)
• Consequence: LINC02306 ENST00000546412.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.67

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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.8 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
LINC02306	ENST00000546412.2	n.538-2430G>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.465 AC: 70515 AN: 151680 Hom.: 19368 Cov.: 31

Gnomad AFR AF: 0.721

Gnomad AMI AF: 0.244

Gnomad AMR AF: 0.463

Gnomad ASJ AF: 0.284

Gnomad EAS AF: 0.820

Gnomad SAS AF: 0.602

Gnomad FIN AF: 0.373

Gnomad MID AF: 0.315

Gnomad NFE AF: 0.302

Gnomad OTH AF: 0.409

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

GnomAD4 genome AF: 0.465 AC: 70607 AN: 151798 Hom.: 19402 Cov.: 31 AF XY: 0.472 AC XY: 35004 AN XY: 74162

Gnomad4 AFR AF: 0.721

Gnomad4 AMR AF: 0.463

Gnomad4 ASJ AF: 0.284

Gnomad4 EAS AF: 0.821

Gnomad4 SAS AF: 0.601

Gnomad4 FIN AF: 0.373

Gnomad4 NFE AF: 0.302

Gnomad4 OTH AF: 0.415

Alfa AF: 0.322 Hom.: 11033

Bravo AF: 0.481

Asia WGS AF: 0.685 AC: 2379 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.011
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1475010; hg19: chr14-26136611;