rs862966

Positions:

• chr14-26008955-T-C
• chr14-26008955-T-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, non coding transcript 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, non_coding_transcript
• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02306	ENST00000546412.2	n.258+117202A>G		intron_variant, non_coding_transcript_variant		3
LINC02306	ENST00000657312.1	n.458+117202A>G		intron_variant, non_coding_transcript_variant

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;